Methods for culturing stem and progenitor cells

ABSTRACT

The present application describes a method of culturing, expanding or growing stem or stem-like cells or induced pluripotent stem cells on a surface, including attaching the cells to the surface through a ligand that binds to the surface and the cells.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. patent applicationSer. No. 13/966,214, filed Aug. 13, 2013, which is a divisional of U.S.patent application Ser. No. 12/814,420, filed Jun. 11, 2010, whichclaims the benefit of priority to U.S. Provisional Patent ApplicationNos. 61/323,779, filed Apr. 13, 2010, and 61/186,310, filed Jun. 11,2009, each of which is hereby incorporated by reference in theirentirety.

BACKGROUND OF THE INVENTION

A problem that exists in the field of culturing or proliferating stemcells, progenitors, induced pluripotent stem cells or other non-adherentcells, is how to culture the cells in a way that will not interfere withlater intended uses, including transplants or downstreamdifferentiation. Unlike most cells that adhere to plastic, which can becultured in plastic growth flasks, stem cells are non-adherent,therefore cannot be grown using traditional methods. Stem cells will,however, grow on layers of fibroblast cells. These “feeder cell” layersprovide a surface for adhesion and feed the cells with a mixture of asyet uncharacterized growth factors that are required for stem cellgrowth and survival. More recently, researchers have been able toculture stem cells by attaching them to components derived from theextracellular matrix, such as matrigel. Stem cells adhere to thesesurface-like substrates but must be cultured in growth media thatcontains both basic fibroblast growth factor (bFGF) and collectedsecretions from fibroblast feeder cells. It is not entirely clear how orwhy these methods promote stem cell proliferation, since they both use amilieu of uncharacterized factors secreted by cells. It has beenreported that stem cells differentiate more quickly when they arecultured over matrigel surfaces. Stem cells grown according to eithermethod, i.e. feeder cells or matrigel plus conditioned media from feedercells, spontaneously differentiate. Differentiating stem cells secretefactors that induce neighboring cells to also initiate differentiation.Therefore, every approximately 7 days, a technician must manuallydissect and harvest only those stem cell colonies or colony portionsthat appear to be undifferentiated. The harvested cells are thenre-plated for continued growth. This procedure is repeated until enoughundifferentiated cells can be harvested for the intended purpose. Thesemethods for culturing stem cells are the state of the art for theindustry.

Virtually any kind of scaled up growth of stem cells or inducedpluripotent stem cells will require the development of new methods thatenable high throughput harvesting of these cells.

The current practice is to grow stem cells on fibroblast feeder cellsfrom which the only method of harvesting is by manual dissection, undera microscope, and isolation of “good” cells, followed by re-plating.This procedure is flawed because it is subjective and time consuming.What is needed are methods for automatable harvesting and automatablemethods for purifying the desired cells from a mixed pool wherein cellsare selected on the basis of molecular recognition rather thansubjective criteria of a technician.

The state of the art methods for culturing stem cells are inadequatebecause they: 1) are labor-intensive; 2) are inherently incompatiblewith large scale growth; 3) depend on uncharacterized factors such asconditioned media; 4) require cells or cellular products for adheringstem cells to growth flasks; and 5) frequently use non-human cells andcellular extracts that can irreversibly change the human stem cells. Asignificant improvement would be if discrete factors that enable stemcell growth were identified. It is thought that if only the necessaryand sufficient growth factors were added, then spontaneousdifferentiation would be minimized. Another significant improvementwould be if cells could be safely harvested in a manner that wascompatible with large scale growth rather than the current method ofmanual dissection under a microscope. Currently, stem cells growing onmatrigel can be harvested by enzymatic cleavage, e.g. using trypsin.Typically, undifferentiated colonies or portions of colonies aremanually dissected then digested with an enzyme such as trypsin orcollagenase. However, trypsin causes significant cell death and serialpassaging of stem cells on matrigel has been reported to cause abnormalkaryotype. This could be due to harvesting with trypsin or may be due tothe fact that matrigel is a mixture of cells and secretions from mousesarcoma cells. Non-human feeder cells have been suspected of alteringthe resultant stem cells so that they are not entirely human. Forexample, it is suspected that glycosylation patterns and otherpost-translational modifications may take on characteristics of thefeeder cell species.

Thus it would be a great improvement over the state of the art ifcell-free methods were developed that support stem cell growth. An evengreater improvement would be if stem cells could be grown and harvestedusing fully characterized, discrete agents wherein as many as possibleare synthetic agents. For producing cells suitable for human therapies,it would be a great improvement over the state of the art if methodswere developed for culturing the cells that is comprised solely ofdefinable factors. Ideally, the defined components should be free ofnon-human components. Recombinant proteins, or synthetic components arepreferred. Antibodies, including polyclonal, monoclonal, humanized,chimeras or derivatives thereof are especially preferred because theirproduction is highly reproducible, they are robust and they can bereadily removed from the harvested cells, for example by affinitydepletion using Protein A or Protein G.

SUMMARY OF THE INVENTION

The present invention is directed to a method of culturing, expanding orgrowing stem or stem-like cells or induced pluripotent stem cells on asurface, comprising attaching the cells to the surface through a ligandthat binds to the surface and the cells. The ligand may bind to thesurface directly or indirectly through an intermediary. The intermediarymay be a chemical linker or another protein or a combination thereof.The protein may be protein A or protein G. In particular, the linker maybe photo or chemically sensitive. And the ligand or the intermediary maybe non-specifically adsorbed to the surface, or may be covalentlycoupled or attached to the surface through an affinity tag-bindingpartner interaction. The ligand may also be linked to a polymer. In aparticular embodiment, the ligand may specifically bind to a polypeptidethat is expressed on the stem or stem-like cells or induced pluripotentstem cells. The polypeptide on the surface of the cell may be MUC1 orMUC1*, SSEA3, SSEA4, Tra 1-81 or Tra 1-60. The ligand may be an antibodyor a growth factor. Preferably, the antibody may specifically bind toPSMGFR or C-10 PSMGFR. Preferably, the growth factor may be wild-typeNM23, or NM23-S120G mutant, or bFGF.

In another aspect, the present invention is directed to a method forculturing stem or stem-like cells or induced pluripotent stem cells,wherein the cells are exposed to a medium containing agents that bind toa peptide having the sequence of PSMGFR. In this respect, the agent maybe an antibody, or the agent may be wild-type NM23 or NM23-S120G mutant.

In yet another embodiment, the present invention is directed to a methodof culturing stem or stem-like cells or induced pluripotent stem cellscomprising exposing the cells to medium containing agents secreted fromMUC1*-positive cancer cells. The MUC1*-positive cells may be T47D,ZR-75-30, or ZR-75-1.

In yet another aspect, the invention is directed to a method ofculturing stem or stem-like cells or induced pluripotent stem cellscomprising exposing the cells to conditioned media from MUC1*-positivecancer cells. The MUC1*-positive cells may be in particular T47D,ZR-75-30, or ZR-75-1.

In one aspect, the surface that is to be used may be preferably notmatrigel, and with the presence of fibroblast feeder cells, nor manualdissection process when the cells are removed.

In another aspect, the present invention is directed to a method ofharvesting cells from cells grown according to the method above,comprising adding a competing molecule that binds to the ligand so thatthe cells are released from binding to the ligand or the surface.

In yet another aspect, the present invention is directed to a method ofharvesting cells from cells grown according to the method indicatedabove, comprising cleaving a linker bound to the surface that isdirectly or indirectly attached to the cells, so that the cells arereleased from the surface.

In yet another aspect, the present invention is directed to a method ofidentifying state of differentiation of cells comprising usinganti-MUC1* antibody to bind to the cells, wherein positive signal foranti-MUC1* antibody indicates pluripotent cell state, and cells showingbinding to non-clipped MUC1 indicates differentiated cell state. Thismethod may further include separating cells from a mixed population ofstem and stem-like cells or induced pluripotent stem cells and newlydifferentiating cells, comprising using anti-MUC1* antibody to bind tothe cells, wherein positive signal for anti-MUC1* antibody indicates apluripotent cell state, and cells showing binding to non-clipped MUC1indicates differentiated cell state. In particular, this method mayfurther include contacting the cells with antibodies to stem orstem-like cell or induced pluripotent stem cell markers, whereinpositive signal for a stem or stem-like cell or induced pluripotent stemcell marker indicates the presence of pluripotent stem cell state. Inparticular, the cells may be contacted with anti-MUC1* and anti-Tra1-81, anti-Tra 1-60, SSEA3 or SSEA4 antibodies.

In yet another aspect, the present invention is directed to a method ofdetecting cancer stem cells using anti-MUC1* antibody to bind to thecells, wherein positive signal for anti-MUC1* antibody indicates cancerstem cells. This method may further include contacting the cells withantibodies to stem cell markers, wherein positive signal for a stem cellmarker indicates the presence of cancer stem cells.

In yet another aspect, the present invention is directed to a method ofmodulating culturing, expanding or growing and inhibitingdifferentiation of stem or stem-like cells or induced pluripotent stemcells on a surface, comprising attaching the cells to the surfacedirectly or indirectly through a ligand that binds to the cells, andexposing the cells to a medium containing agents that bind to a peptidehaving the sequence of PSMGFR. The agent may dimerize MUC1* to promotegrowth and inhibit differentiation, or the agent may inhibitdimerization of MUC1* to promote differentiation.

In yet another aspect, the present invention is directed to a method ofseparating cell types, comprising: creating a spatial address on asurface for a variety of ligands having affinity for a different celltype or for specific markers that identify a cell stage or type; andadding the cells to the surface, wherein the cells are spatiallyseparated depending on which ligand the cells bind. The surface may be aparticle or a nanoparticle.

In yet another aspect, the present invention is directed to a method ofimplanting into a host body, a surface having ligands attached that areligands of stem or stem-like cells or induced pluripotent stem cells.The host may be a patient. In particular, the ligands may be growthfactors for the host's stem or stem-like cells or induced pluripotentstem cells.

In yet another aspect, the present invention is directed to a method ofimplanting into a host body, a surface having cells attached throughligands that bind to the surface and the cells.

In yet another aspect, the present invention is directed to a method ofproliferating stem or stem-like cells or induced pluripotent stem cellsin vivo, comprising administering to a host body a surface havingligands attached that are ligands of stem or stem-like cells or inducedpluripotent stem cells.

In yet another aspect, the present invention is directed to acomposition comprising: a surface on which is bound protein A or proteinG via an affinity interaction, wherein the protein A or protein G isbound to an antibody specific for a polypeptide expressed specificallyon a stem or stem-like cell or induced pluripotent stem cell, and aMUC1* dimerizing agent. The affinity interaction may be via NTA-Niinteraction to the surface. The polypeptide may be MUC1 or MUC1*, SSEA3,SSEA4, Tra 1-81 or Tra 1-60. The MUC1* dimerizing agent may be wild-typeNM23 or NM23-S120G mutant.

In yet another aspect, the present invention is directed to a method ofproliferating stem or stem-like or induced pluripotent stem cell,comprising: contacting a surface on which is bound protein A or proteinG via an affinity interaction, wherein the protein A or protein G isbound to an antibody specific for a polypeptide expressed specificallyon a stem or stem-like cell or induced pluripotent stem cell, with asample containing the cells and with a MUC1* dimerizing agent.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows that human embryonic stem cells (H9s) attached to matrigelgrow essentially 100% pluripotent (OCT4+) when cultured in anti-MUC1* inminimal media, compared to lesser cell numbers and more differentiationwhen cultured in the standard bFGF and conditioned media from fibroblastfeeder cells. DAPI stains the nuclei of all cells. Dotted lines demarkthe border of the undifferentiated portion of the colony. In wellstreated with anti-MUC1*, undifferentiated stem cells grew to the limitsof the wells.

FIG. 2 shows that after 18 passages of human embryonic stem cells onmatrigel in anti-MUC1* and minimal media alone, karyotype of BG01v/hOGwas unchanged.

FIGS. 3A-3D show that human embryonic stem cells cultured on matrigel inanti-MUC1* and minimal media alone, were able to differentiate down the3 germlines: FIG. 3A) OCT4-negative indicates that the cells havedifferentiated; FIG. 3B) positive for alpha-fetoprotein indicatesdifferentiation along the endoderm germline; FIG. 3C) positive forNestin indicating differentiation down the ectoderm germline; and FIG.3D) positive for smooth muscle actin, indicating differentiation downthe mesoderm germline.

FIG. 4 shows that surfaces coated with anti-MUC1* antibody supports stemcell growth whether cultured in minimal stem cell media alone or bFGFplus conditioned media from fibroblast feeder cells. An irrelevantantibody coated onto a different surface did not cause stem celladhesion and cells died within 24 hours.

FIGS. 5A-5D show photos of human stem cells attached to matrigel aftermultiple passages in culture containing only anti-MUC1* and minimalmedia. FIGS. 5A and 5C show DAPI staining the nuclei of all the cellsand FIGS. 5B and 5D show a 1:1 correlation to OCT4 staining. Togetherthey show that all the cells retain OCT4+, which indicates pluripotency.

FIGS. 6A-6H show photos of hu ES H9s cells growing on anti-MUC1*antibody surfaces: A) cultured in minimal media alone at day 3 (FIG. 6G)and day 7 (FIG. 6H); B) minimal media plus 80 ng/ml anti-MUC1* at 3 days(FIG. 6E) and 7 days (FIG. 6F); C) in 4 ng/ml bFGF and 50% conditionedmedia from HS27 fibroblasts at day 3 (FIG. 6C) and day 7 (FIG. 6D).FIGS. 6A and 6B show cells from well A and B were harvested by addingfree PSMGFR (MUC1* extra cellular domain) peptide, which released thecells from the surface; cells were re-plated on fresh anti-MUC1*antibody surfaces where they attached and proliferated.

FIG. 7 is a graph of stem cell growth on surfaces coated with anti-MUC1*antibody or the same antibody coupled to beta-cyclodextrin. It showsenhanced cell adhesion and growth when antibody is coupled to thedextrin.

FIG. 8 shows that hu ES cells can be cultured by attaching them tosurfaces coated with antibodies that bind to stem cell surface markerproteins SSEA4 and Tra 1-81 if cultured in minimal media plus 80 ng/mlof anti-MUC1* antibody.

FIG. 9 shows that hu ES cells on matrigel grow at least as well as thestate of the art when they are cultured in minimal media plus NM23. Thegraph compares the growth of hu ES H9 cells on Matrigel when they arecultured in the standard 4 ng/ml bFGF plus HS27 conditioned media fromfibroblasts (Control) and growth in minimal stem cell media plus NM23 atthe concentrations indicated. Percent undifferentiated growth wascalculated by a blinded count of both undifferentiated anddifferentiated colonies, then calculated as percent. Only cells thatwere totally undifferentiated were scored undifferentiated.

FIG. 10 shows hu ES cells growing on surfaces coated with anti-MUC1*covalently coupled to cyclodextran and cultured until ready to split inminimal media plus NM23 at indicated concentrations. One set of cellswas first cultured in 4 ng/ml bFGF plus 50% HS27 fibroblast conditionedmedia (CM) for the first 24 hours. The graph shows that bFGF and CM donot benefit cell growth or differentiation state if adequate amounts ofNM23 are added.

FIGS. 11A-11G show that stem cells adhere and are cultured on surfacescoated with NTA-Ni, to which first were bound histidine-tagged ligandsNM23, an RGD peptide, and Protein G, followed by anti-SSEA4 and Tra1-81. Hu ES H9 cell growth and colony formation followed.Undifferentiated and differentiated colony numbers counted at day 3 wereplotted in FIG. 11A. Photos of representative stem cells colonies thatwere plotted are shown in FIGS. 11B-11G.

FIG. 12 shows that conditioned media from MUC1*-positive cancer cells(Ca CM) promotes the growth of and inhibits differentiation of hu EScells to a far greater extent than the standard fibroblast conditionedmedia (CM). Further, NM23 worked much better than the standard bFGF whenadded to Ca CM.

FIGS. 13A-13C show photos of hu BG01v/hOG ES cells growing on adsorbedsupernatant from hybridoma clones each secreting a different monoclonalantibody. Monoclonal antibodies that best enable stem cell adhesion areidentified in this way.

FIG. 14 is a graph of an ELISA assay in which hybridoma supernatantswere tested for their ability to bind to deletion mutations of thePSMGFR peptide that were missing 10 amino acids from either the N- orC-terminus. The hybridomas that enabled stem cell attachment to asurface coated with their supernatant, also showed binding to the C-10PSMGFR peptide (GTINVHDVETQFNQYKTEAASRYNLTISDVSVSDV). We reasoned thatantibodies that bound to the more distal portions of the MUC1* extracellular domain would better enable stem cell attachment to surfaces.

FIGS. 15A-15L show photos of ICC staining of H9 human embryonic stemcells before and after they began to differentiate. Anti-MUC1* stainedall cells of undifferentiated colonies and co-localized with OCT4, whichis the gold standard indicator of pluripotency (FIG. 15A, 15B). VU4H5antibody that identifies MUC1-full-length did not stain any of theundifferentiated cells. FIG. 15C. However, when the cellsdifferentiated, the reverse MUC1 pattern was detected. No MUC1* stainingor OCT4 staining was observed (FIG. 15D, 15E). But every cell stainedpositive for the full-length MUC1 (FIG. 15F). Similarly,undifferentiated stem cells stained positive for NM23, the ligand ofMUC1* and NM23 exactly co-localized with MUC1*, and OCT4 (FIGS.15G-15L).

FIGS. 16A-16D show that anti-MUC1* antibody added to stem cell growthmedia increases the growth of human hematopoietic stem cells (HSCs).

FIG. 16E illustrates that FACS analysis shows that the number of cellsthat remained hematopoietic stem cells, CD34+/CD38−, increased withincreasing anti-MUC1* concentration. Conversely, the number of cellsthat had progressed to the next progenitor stage, CD34+/CD38+ increasedas the concentration of anti-MUC1* decreased. These results show thatstimulation of MUC1* growth factor receptor inhibited differentiation ofHSCs.

FIGS. 17A-17B show FACS scans of neural stem cells (FIG. 17A) and fetalliver cells (FIG. 17B). Cells were obtained from the vendor andimmediately stained with both a fluorescently labeled anti-MUC1*antibody and a labeled antibody (HPMV) that recognizes the distalportion of full-length MUC1. The FACS scans show MUC1 is mostly clippedto MUC1* on both types of early progenitors. Subsequent experimentsshowed that anti-MUC1* stimulated the growth of both types of cells in aconcentration dependent manner.

FIG. 18 is a plot of the growth of fetal liver cells as a function ofanti-MUC1* concentration that shows that MUC1* progenitor cells can beisolated and expanded by stimulating the MUC1* receptor.

FIG. 19 is a plot of stem cell colonies after hu ES H9 cells were platedon either anti-MUC1* or anti-SSEA4 antibodies that were coated onto12-well plates, then cultured in either 8 nM NM23 or 4 ng/ml bFGF plus50% HS27 fibroblast conditioned media.

DETAILED DESCRIPTION OF THE INVENTION

In the present application, “a” and “an” are used to refer to bothsingle and a plurality of objects.

As used herein, “MUC1 Growth Factor Receptor” (MGFR) is a functionaldefinition meaning that portion of the MUC1 receptor that interacts withan activating ligand, such as a growth factor or a modifying enzyme suchas a cleavage enzyme. The MGFR region of MUC1 is that extracellularportion that is closest to the cell surface and is defined by most orall of the PSMGFR, as defined below. The MGFR is inclusive of bothunmodified peptides and peptides that have undergone enzymemodifications, such as, for example, phosphorylation, glycosylation andso forth.

As used herein, “Primary Sequence of the MUC1 Growth Factor Receptor”(PSMGFR) refers to peptide sequence that defines most or all of the MGFRin some cases, and functional variants and fragments of the peptidesequence. The PSMGFR is defined as SEQ ID NO:1, and all functionalvariants and fragments thereof having any integer value of amino acidsubstitutions up to 20 (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, or 20) and/or any integer value of amino acidadditions or deletions up to 20 at its N-terminus and/or C-terminus. A“functional variant or fragment” in the above context refers to suchvariant or fragment having the ability to specifically bind to, orotherwise specifically interact with, ligands that specifically bind to,or otherwise specifically interact with, the peptide of SEQ ID NO:1,while not binding strongly to identical regions of other peptidemolecules identical to themselves, such that the peptide molecules wouldhave the ability to aggregate (i.e. self-aggregate) with other identicalpeptide molecules. One example of a PSMGFR that is a functional variantof the PSMGFR peptide of SEQ NO:1 is SEQ ID NO:2, which differs from SEQID NO:1 by including an —SPY— sequence instead of the —SRY—.

As used herein, “MUC1*” refers to the MUC1 protein with the N-terminustruncated such that the extracellular domain is essentially comprised ofthe PSMGFR (SEQ ID NO: 1).

As used herein, a “surface” as used in the context of the cell beingbound to a surface can be a solid substrate, or porous substrate orother non-solid substrates.

As used herein, “minimal media” can be any media that contain theminimum nutrients possible for cell culture, generally without thepresence of a mixture of undefined agents, such as conditioned mediafrom cells, or serum from a live host. As used herein, “minimal stemcell growth media” can be any media that contain the minimum nutrientspossible for stem cell or stem-like cell culture, This is also referredto as minimal media or MM. As can be seen minimal media as used in thepresent invention is not limited to the exemplified minimal media andcan encompass numerous types of solutions with defined components.

As used herein, “stem-like” cells have some of the characteristics ofstem cells. For example, they have some ability to self-renew. Theyeither: a) express, or are induced to express, OCT4, SOX2, and NANOG, orKLF4; orb) they express high levels of MUC1* on their surface. Examplesof stem-like cells include but are not limited to progenitor cells,multipotent stem cells, cells undergoing process to induce pluripotency,cancer cells, cancer stem cells, hematopoietic stem cells, iPS, and someantibody producing hybridoma cells.

As used herein, “induced pluripotent stem cells” or “iPS” refers to atype of pluripotent stem cell artificially derived from anon-pluripotent cell, typically an adult somatic cell, by inducing a“forced” expression of certain genes.

As used herein, “MUC1* stimulator” refers to any molecule that is ableto activate the activity of MUC1*, such as dimerization of MUC1* orcleavage of MUC1 to form MUC1*.

Sequence Listing Free Text

As regards the use of nucleotide symbols other than a, g, c, t, theyfollow the convention set forth in WIPO Standard ST.25, Appendix 2,Table 1, wherein k represents t or g; n represents a, c, t or g; mrepresents a or c; r represents a or g; s represents c or g; wrepresents a or t and y represents c or t.

(SEQ ID NO: 1) GTINVHDVETQFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGAdescribes the membrane proximal extracellular region of MUC1 from aminoacid 1110 to 1155 (PSMGFR).GTINVHDVETQFNQYKTEAASPYNLTISDVSVSDVPFPFSAQSGA (SEQ ID NO:2) describes avariant of the membrane proximal extracellular region of MUC1 from aminoacid 1110 to 1155 (variant of PSMGFR).QFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA (SEQ ID NO:3) describes the PSMGFRsequence with ten amino acids at the N terminus deleted (N-10 PSMGFR).

GTINVHDVETQFNQYKTEAASRYNLTISDVSVSDV (SEQ ID NO:4) describes the PSMGFRsequence with ten amino acids at the C terminus deleted (C-10 PSMGFR).

Stem or Stem-Like Cell or Induced Pluripotent Stem Cell on a Surface

The present invention discloses methods for culturing or expanding stem,or stem-like cells or induced pluripotent stem cells and progenitorsthat involve attaching ligands to cell surface proteins onto solidsupports that can either hold growth medium or that can be added togrowth medium.

The present invention discloses new methods and surfaces for culturingcells. The methods are especially useful for growing and maintainingcells that are not adherent. These methods are particularly useful forculturing stem, stem-like and progenitor cells.

Surfaces

The present invention discloses new surfaces and methods for growingcells. These surfaces are particularly useful for culturing non adherentcells, stem cells and stem-like cells, including induced pluripotentstem (iPS) cells and some progenitor cells. Methods disclosed hereinsolve the problem of how to retain valuable cells while exchanging cellculture media. Many of the existing cell culture methods work foradherent cells because they attach to the flask surface. Old liquidmedium can be removed and replaced with new medium without disturbingthe cells that are attached to the surfaces of the containment vessel.Some methods of the invention are also useful in that they allow for theretention of valuable growth factors, while less expensive factors thatneed to be replaced more frequently are exchanged. Other methods of theinvention provide for greater surface area for cell attachment andthereby increase the yield of cells while using a relatively small spaceand a small volume of culture medium. The methods in general involveattaching, either directly or indirectly, ligands to a surface whereinthe ligands are able to bind to molecules on the cell surface.

Surfaces that are suitable for use with these methods can be membranesor porous in nature. Surfaces described herein can be polymers, surfacescoated with polymers, cyclodextrin or cyclodextran. The surfaces may bespatially addressable surfaces, surface of beads, particles, ornanoparticles. The beads, particles or nanoparticles can be free insolution or connected by intervening molecules. For example a membrane,can be comprised of a polymeric substance and may have attached theretobeads or particles bearing ligands that promote binding between cellsand the surface. The invention includes the use of these surfaces for invitro, ex vivo and in vivo growth. Surfaces of the invention can be usedto culture cells in vitro. Alternatively, surfaces of the invention canbe implanted in a host. The surfaces can bear cells, such as stem cells,that are implanted as a therapy. For example, surfaces of the inventionwith or without growing stem cells attached can be transplanted so thatthe surface increases the efficiency of engraftment. In another case,the transplanted surface bears ligands to recruit the host's own cellsor stem cells to an area or to promote the growth of targeted cells atthat location. For example, surfaces that attract and promote the growthof stem cells can be inserted into a joint to encourage the replacementof cartilage. Surfaces of the invention can be shaped or coated onto ascaffold such that the cells eventually form a 3-dimensional form. Forexample, a material can be made into the shape of an ear then coatedwith one of the surfaces described herein that enable to attachment andgrowth of stem or stem-like cells that eventually develop into moremature cells or tissues in the shape of the scaffold. It is furtherenvisioned that surfaces and compositions of the invention can be usedto coat implantable devices, which may be structured or unstructuredporous or solid surfaces. Said devices can deliver or recruit stem orprogenitor cells to an area for purposes of repair or regeneration oftissues or cells. Stents for example can be coated with any of thesurfaces or compositions of the invention to either repair or regenerateblood vessels. Stents coated with surfaces of the invention, e.g.NM23-S120G and to which stem or progenitor cells were attached could beimplanted in a host or person to deliver cells or growth factors thatstimulate the host's own cells. The methods can be carried out in vitro,ex vivo or in vivo.

Ligands

Ligands that promote binding of cells to the surface or that stimulatecellular proliferation can be attached directly to surfaces orindirectly, e.g. to polymers attached to surfaces. For example,antibodies that recognize cell surface receptors can be covalentlyattached to a polymer such as cyclodextrin or cyclodextran that has beenattached or adsorbed onto a surface, see Examples 6, 10-12 and FIGS. 7,10. Ligands that have some affinity for molecules on the cell surfaceare optionally attached to these surfaces to promote the attachment andgrowth of cells. The ligands may specifically bind to on the cellsurface, such as growth factor receptors. Ligands may be proteins,peptides, small molecules, antibodies, polyclonal or monoclonalantibodies, bispecific antibodies, mono-valent or bi-valent antibodies,antibody derivatives such as Fabs, single chain antibodies, geneticallyengineered derivatives or derivatives in which the variable domain of anantibody is inserted into another protein such that it as able tospecifically bind to its target. Alternatively, ligands need not havespecific affinity for cell surface molecules. For example, ligandsattached to the surface may cause cells to adhere to the surface throughnon-specific interaction. Non-specific interactions may be chemical orbiological in nature. Surfaces derivatized with hydrophilic moietiessuch as hydroxyls or hydrophobic headgroups such as methyl groups mayretain cells non-specifically via hydrophobic interaction. Surfacesbearing charged chemical or biological entities may adsorb cells throughionic interaction. Cells may additionally be captured by surfacesbearing entities that have some specificity for cells, including but notlimited to RGD sequence containing peptides, poly-Lysine, positively ornegatively charged surfaces, collagen, laminin, and other extracellularmatrix components, including matrigel and matrigel-like substances.Cells can also be captured by other types of chemically modifiedsurfaces. For example, surfaces coated with NTA-Ni and other metalchelates non-specifically bind cells and stem cells, see Example 15 andFIG. 12.

In a preferred embodiment, moieties that have specific affinity formolecules on the cell surface are attached to surfaces to facilitate theattachment of stem cells. For example, antibodies that bind to cellsurface proteins that are specific markers of stem cells, such as SSEA3,SSEA4, or Tra 1-81 or Tra 1-60, are attached to surfaces. Stem cellsadhere to these surfaces via the specific interaction between their cellsurface proteins and their cognate antibody on the growth plate. Cellscan then be cultured by either standard methods or novel methods of theinvention that stimulate MUC1*, see Examples 1-4, 8-10, 12 and FIGS.1-10. In another instance the ligand that is attached to the surface isa growth factor or a portion of a growth factor. In another instance,the ligand attached to the surface is an antibody, or a portion of anantibody that recognizes a cell surface molecule, which could be agrowth factor receptor. In another instance, a ligand complex isattached to or immobilized on surfaces wherein at least one member ofthe complex has affinity for a cell surface molecule or provides thecell with an agent that modulates the cell's growth or differentiation.For example, protein G can be adsorbed onto, or specifically attachedto, a surface via a histidine tag NTA-Ni interaction and an antibodythat recognizes a stem cell surface marker is attached to the surface byits interaction with protein G, see Example 14, FIGS. 11A-11G.

Mixed Surfaces

In some cases, it is desirable to have surfaces that present a mixtureof ligands and components. These may be biological or chemical in natureor may be a mixture of biological and chemical components. For example,surfaces can be coated with a mixture of a growth factor, or equivalentactivating antibody plus components of the extracellular matrix such ascollagen or laminin. Surfaces coated with a mixture of laminin andgrowth factors or antibodies also promoted stem cell attachment andgrowth. For example, we have shown that surface coatings comprised ofcollagen or laminin and an antibody specific for a cell surface markerare useful for growing stem and stem-like cells.

In another example, laminin or collagen is mixed with a ligand of a cellsurface marker. Experiments showed that mixing laminin with anti-MUC1*reduced the amount of antibody that was required for stem cellattachment and cell growth and normal stem cell colonies developed. Inanother aspect of the invention, mixed species are attached to a surfacewherein one or more components are ligands that facilitate attachment ofthe cell to the surface and the other(s) is a component that providesthe cell with an agent that affects the function of the cell. Examplesof functional agents that can be attached to the surface include but arenot limited to agents that promote growth, differentiation, or inducepluripotency.

Methods for Ligand Attachment

Ligands that promote cellular adhesion or are growth factors can beattached to surfaces in a variety of ways, including but not limited tocovalent coupling, for example using EDC/NHS or maleimide couplingchemistries. Alternatively, ligands of the invention can be attached tosurfaces via a non-covalent interaction or an affinity interaction. Forexample, ligands of the invention can be histidine tagged then attachedto the surface via a nitrilo tri-acetic acid-nickel (NTA-Ni) moiety.Affinity tag interactions can be used to generate a growth surfacesuitable for culturing cells. For example, an NTA-Ni moiety is attachedto a cell culture flask and a histidine tagged ligand is captured byNTA-Ni. The ligand either directly or indirectly binds to a cell surfacereceptor to anchor the cell to the surface. If the ligand is also agrowth factor, then it serves to both cause cellular adhesion andpromotes proliferation, see Example 14, FIGS. 11A-11G.

In one embodiment, the ligand is Protein G or A to which is bound anantibody that recognizes a cell surface receptor, such as MUC1* or FGFR(fibroblast growth factor receptor). The Protein G or A can benon-specifically adsorbed onto a surface, covalently coupled or attachedthrough an affinity tag-binding partner interaction. For example, cellculture flasks can be coated with an NTA-Ni moiety so that ahistidine-tagged Protein G or A can be captured by the surface. Anantibody to a cell surface receptor is then added, whereupon it binds tothe Protein G or A that is immobilized on the surface.

In another aspect, ligands and agents that are attached to the surfacescan be attached to the surface in such a way that they can be releasedfrom the surface to change the local environment or so that the cell canconsume the agent. Agents can be attached to the surface such that theyare released from the surface as they degrade or they can be released inresponse to a stimulus. For example, agents can be attached to a surfaceusing photo-sensitive or chemically sensitive linkers so that the agentcan be released in response to light or via a chemical signal. Somelinkers cleave in response to changes in pH. Genes or gene products,such as OCT4, NANOG, SOX2, KLF4 or NM23 that induce either pluripotencyor genes or their products that induce differentiation, such as miR-145(micro RNA) can be added to the media or attached to surfaces. They canbe released from the surfaces by degradation over time or in response toa specific signal such as a specific wavelength of light to cleave theattachment bonds.

In a preferred embodiment, the ligand that is attached to or immobilizedon the surface is a growth factor that recognizes a growth factorreceptor on the cell surface. Antibodies that activate growth factorreceptors on the cell surface can be attached to surfaces using any ofthe methods previously described or combinations thereof. In oneinstance, the growth factor is fibroblast growth factor (FGF) or basicfibroblast growth factor (bFGF) and the molecule on the cell surface forwhich the ligand has an affinity is the fibroblast growth factorreceptor (FGFR). Alternatively, the ligand can be an antibody thatrecognizes FGFR. In another aspect of the invention, the growth factoris epidermal growth factor (EGF) and the molecule on the cell surfacefor which the ligand has an affinity is the epidermal growth factorreceptor (EGFR). In another aspect, the affinity ligand is stem cellfactor (SCF) or another agent, including an antibody, that activatesc-Kit/SCF-R. Ligands that are attached to the growth surface can also beFlt 3 ligand, thrombopoetin (TPO), IL-2, IL-3, IL-n or antibodies thatsimulate their affect on their cognate receptors.

MUC1* Ligands

In a more preferred embodiment, the ligand attached to the growthsurface has an affinity for the MUC1 cell surface protein. In a yet morepreferred embodiment, the ligand has affinity for the PSMGFR portion(MUC1*) of the protein. And in a still more preferred embodiment, theligand induces dimerization of MUC1*. In one instance the ligand is ananti-MUC1* antibody (Examples 1, 4, 7, 10, and FIG. 1, FIGS. 6A-6B,FIGS. 6E-6H, and FIG. 8. In another instance the ligand is NM23 or avariant such as S120G, or any other mutant or derivative that prefersdimer formation or functions as a dimer, see Examples 9, 12, 14, 15, 20and FIGS. 9, 10, 11A-11G, 12 and 19. The surface may be configured suchthat NM23 is presented to the cell as a dimer. In another instance, theligand attached to the growth surface is an antibody that binds to theextracellular domain of MUC1. Antibodies that bind to the portion ofMUC1 that remains attached to the cell surface after the tandem repeatdomain is cleaved and shed from the cell surface are preferred. Forexample, bivalent antibodies that bind to the PSMGFR sequence of MUC1activate the growth factor receptor function of cleaved MUC1 andstimulate cell proliferation. Polyclonal or monoclonal antibodiesgenerated by immunization with at least a portion of the PSMGFR peptideare attached to the surfaces to both promote the attachment of cells tothe surface and to stimulate growth of the cells via activation of theMUC1* growth factor receptor.

Either polyclonal or monoclonal antibodies, as well as both natural andnon-natural antibody derivatives, can be generated or selected such thatthey are better suited for stem cell adhesion than antibodies generatedwith, or selected for affinity to, the entire PSMGFR sequence.Polyclonal antibodies generated by immunizing with rabbits with apeptide corresponding to the sequence of the MUC1* extra cellular domainbut with the 10 amino acids proximal to the cell surface deleted, “C-10PSMGFR” generated antibodies that were more efficient in promoting stemcell adhesion than antibodies generated against either the full PSMGFRpeptide or an “N-10 PSMGFR” (QFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA) (SEQID NO:3), that had the most distal 10 amino acids deleted, see Example16 and FIGS. 13A-13C, 14. Antibodies that have improved ability to bindstem cells can also be isolated from polyclonals raised against the fullPSMGFR peptide by affinity purifying them over surfaces that present theC-10 PSMGFR peptide or other N-terminal fragment.

Hybridoma clones that secreted a monoclonal antibody that bound to theC-10 PSMGFR peptide but not the N-10 PSMGFR peptide were shown tofacilitate stem cell adhesion to surfaces, see FIGS. 13 A-C, FIG. 14. Incontrast, monoclonal antibodies that bound to N-10 PSMGFR peptides butnot to the C-10 PSMGFR peptides barely enabled stem cell adhesion. Bothmonoclonal antibody types were able to stimulate cell growth when theywere added to the culture media.

In a preferred embodiment, stem cells are cultured over a surface thatpresents NM23 which is a ligand of the MUC1* growth factor receptor.NM23 can be directly or indirectly attached to surfaces. In one aspectof the invention, NM23 or the S120G mutant that prefers dimerization arenon-specifically adsorbed onto surfaces for cell growth, see Example 15,FIG. 12. In another aspect of the invention, a surface is firstderivatized with an affinity tag binding partner such as NTA-Ni thatbinds to histidine-tagged proteins or peptides. Histidine-tagged NM23 isthen non-covalently coupled to the NTA-Ni surface. MUC1*-positive cellssuch as stem cells and some progenitors are then added to the NM23surfaces, whereupon the cells adhere to the surfaces and grow. In astill more preferred embodiment, NM23 S120G mutant is covalently coupledto cyclodextran.

Methods for Harvesting

In another aspect of the invention, novel methods for harvesting cellsfrom surfaces of the invention are described. The invention includesthese harvesting methods that are useful for surfaces of the presentinvention as well as for many other cell growth systems. The inventionalso includes the use of standard harvesting methods, such as manualdissection and enzymatic cleavage, with the novel surfaces of theinvention. Some of the cell harvesting methods depend on the identity ofthe surface components. For example, cells growing by adsorption ontoantibody surfaces can be released by the addition of excess peptidehaving the same sequence as the antibody epitope. For example, if theantibody recognizes the extracellular domain of MUC1*, then the cellscan be released by adding an excess of a peptide having some or all ofthe sequence of the extracellular domain of MUC1*. The free peptidecompetes with the MUC1* receptor on the cells for binding to the surfaceattached antibody. Binding of the peptide to the antibody releases thecell, see Example 4, FIGS. 6A-6B. Cells cultured on surfaces presentingantibodies that are attached to a surface by binding to Protein G or Aare released from the surface by adding excess Fc portions or an excessof an irrelevant antibody. Since Protein G binds to Fc domains, free Fccompetes with the cognate antibody for binding to the surface-attachedProtein G or A and releases the antibody-complexed cells. Cells culturedon surfaces with ligands attached by an affinity tag-binding partnerinteraction are released by adding an agent that interferes with theaffinity tag-binding partner interaction or by adding an excess of theportion of the affinity tag that interacts with the binding partner. Forexample, cells growing on histidine-tagged ligands bound to NTA-Nisurfaces are released by adding either imidazole, an irrelevanthistidine peptide, or an excess of at least a portion of the bindingpartner of the surface attached ligand. In the case of NM23 surfaces,cells can be released by adding an excess of a peptide having a sequenceessentially the same as at least a portion of the extracellular domainof MUC1*, such that addition of the excess peptide competes with theMUC1* cell surface receptor for binding to the surface attached NM23,thus releasing the cells. Alternatively, NM23 is made with an affinitytag that facilitates attachment to a surface. Strategies that interferewith the interaction between the affinity tag and the surface releasethe NM23 and the attached cell from the surface. Similarly, His-taggedProtein G (plus an antibody) or His-tagged NM23 can be released from thesurface by adding: a) imidazole (at 0.5M); or b) excess of (His)₆peptide.

Any affinity tag, binding partner pair can be used for the attachment ofligands to the surface and interruption of the affinity tag bindingpartner interaction will release the stem cells from the surface.Examples of suitable affinity tag, binding partners pairs include butare not limited to NTA-Ni/histidine tag, glutathione/GST fusion,maltose/maltose binding protein and biotin/streptavidin.

Growth Media

The surfaces and harvest methods described herein are compatible withstandard stem cell culture methods as well as novel methods. Thestandard stem cell culture media requires the addition of exogenousbasic fibroblast growth factor (bFGF) and growth over fibroblast feedercells because stem cell growth until now has required as yetunidentified growth factors that are secreted by these cells. Stem cellscan also be grown over matrigel according to standard protocol, exceptthat in addition to bFGF, conditioned media from fibroblast feeder cells(CM) must be added to roughly 30-50% of the media. Inactivated humanforeskin (HS27) fibroblast feeder cells are typically used for thegrowth of embryonic stem cells.

We have demonstrated that standard growth media are compatible withgrowth over surfaces of the invention, Example 4, FIGS. 6C-6D andExample 3, FIG. 4. Like growth over matrigel, bFGF mediated growth alsorequires fibroblast conditioned media to support stem cell growth on theinventive surfaces described herein. Preferred are culture mediacontaining MUC1* stimulators or dimerizing agents. Either antibodiesthat recognize the PSMGFR peptide; or NM23, wild type or mutant S120G,are preferred growth factors and can substitute for bFGF and fibroblastconditioned media, see FIGS. 6A-6H, 9, 10, 11A-11G and 12. The growth ofhuman embryonic stem cells, attached to Matrigel, Cell Start(Invitrogen), Geltrex (Invitrogen) or any of the surfaces of theinvention is consistently better when either anti-MUC1* antibodies orNM23-S120G is added to minimal stem cell media in place of bFGF and HS27conditioned media; growth rate, colony morphology and inhibition ofdifferentiation is consistently better when MUC1* stimulators replacebFGF plus conditioned medium (CM).

Conditioned media collected from growing MUC1*-positive cancer cellsincreases stem cell growth and colony formation, while inhibitingdifferentiation. Human stem cells growing on matrigel, NTA-Ni,anti-MUC1* antibodies or NM23 surfaces were cultured in minimal stemcell media plus conditioned media collected from growing MUC1*-positivecancer cells. Conditioned media from T47D cells, which areMUC1*-positive breast cancer cells, when added to NM23-S120G, oranti-MUC1* antibodies or bFGF greatly improved stem cell growth, colonyformation and inhibition of differentiation compared to conditionedmedia from HS27 fibroblast feeder cells, see Examples 14, 15, and FIGS.11A-11G, 12. The surfaces and harvest methods described herein can beused for cells other than stem cells.

Anti-MUC1* Antibodies for Cell Sorting

Purification: Pure populations of pluripotent stem cells can be purifiedfrom mixed populations of cells. Massive stem cell growth may generatesome stem cells that have spontaneously differentiated. Therefore, highthroughout methods for capturing the desired pluripotent cells anddisgarding the differentiated ones may be necessary. MUC1* is a cellsurface marker for pluripotency that is lost before OCT4 when cellsinitiate differentiation. Pure populations of pluripotent(MUC1*-positive) stem cells can be isolated from mixed populations bycapturing them on a column derivatized with anti-MUC1* antibody.Conversely, the MUC1* affinity column will be used to removeMUC1*-positive cells from differentiated cells prior to transplantationto reduce the risk of teratoma formation.

In many cases, it is desirable to separate stem and progenitor cellsaccording to their stage of differentiation. We previously showed thatpluripotent stem cells present the clipped, MUC1* form and not thefull-length MUC1 protein; after differentiation begins, MUC1 cleavagestops and the cells are mostly MUC1* negative and positive for thefull-length form. Many antibodies are available that bind to the tandemrepeat units of full-length MUC1, e.g. commercially available VU4H5 orHMPV antibodies. Cleavage of MUC1 to the growth factor receptor form,MUC1*, releases these portions from the cell surface, so antibodiesagainst the tandem repeats would not stain MUC1*. Although the PSMGFRsequence is present in both MUC1 and its clipped form (MUC1*),antibodies against the PSMGFR sequence do not bind to the full-lengthMUC1 because the epitope is masked. FIG. 15 A-L shows photos ofimmuno-cytochemical (ICC) staining of H9 human embryonic stem cellsbefore and then after they began to differentiate. A rabbit polyclonalantibody raised against the full PSMGFR peptide stained virtually everycell of an undifferentiated colony. OCT4, which is the gold standardindicator of pluripotency for stem cells exactly co-localized with theanti-MUC1* (also called anti-PSMGFR) antibody staining, FIG. 15 A,B. theVU4H5 antibody that binds to the distal tandem repeats ofMUC1-full-length did not stain any of the undifferentiated cells, FIG.15 C. However, when these same cells were allowed to differentiate bywithholding bFGF for 14 days, the reverse MUC1 pattern was observed. NoMUC1* staining or OCT4 staining was observed, FIG. 15 D,E, but everycell stained positive for the full-length MUC1, FIG. 15 F. Similarly,undifferentiated stem cells stained positive for NM23, the ligand ofMUC1* and NM23 exactly co-localized with MUC1*, FIGS. 15 G-I and OCT4,FIG. 15 J-L. Cleavage enzymes MMP14, MMP16, and ADAM-17 have beenimplicated in the cleavage of MUC1. They also co-localize with MUC1* onundifferentiated stem cells, Hikita et al, PLoS ONE, 2008.

Consequently, anti-MUC1* antibodies optionally in combination withothers including antibodies against NM23, MMP14, MMP16, ADAM-17 and OCT4can be used to identify and isolate pluripotent stem cells from a mixedpool. Antibodies against SSEA3/4 or Tra 1-81/1-60 may also be used inconjunction with anti-MUC1* antibodies to identify pluripotent stemcells. Pools of undifferentiated and differentiated stem cells can bestained with antibodies that bind to the PSMGFR peptide and antibodiesthat bind to the portion of MUC1 that is released when it is clipped.Standard cell separation methods such as FACS (fluorescence activatedcell sorting) can then be used to separate out MUC1* presenting cellsfrom those that present the full-length form of the protein. In somecases, it is desirable to remove those stem cells that havedifferentiated from those that remain pluripotent. In other cases, it isdesirable to remove those stem cells that remain pluripotent(MUC1*-positive) because those could increase the risk of teratomaformation if transplanted into a host. Combinations of anti-MUC1*antibodies, i.e. anti-PSMGFR antibodies and NM23 antibodies can also beused to identify pluripotent stem cells and also to identify thoseprogenitor cells that can be expanded by MUC1* stimulation.

Cancer Stem Cells Sorting Depleting

Cancer cells increase expression of MUC1*, but not MUC1-full-length,when they acquire resistance to chemotherapy drugs. These cells that areresistant to chemotherapy are also called cancer stem cells. Therefore,anti-MUC1* antibodies optionally combined with other antibodiesincluding antibodies against NM23, MMP14, MMP16, ADAM-17 and OCT4, canbe used to identify cancer stem cells. In one embodiment of theinvention, anti-MUC1* antibodies and combinations of these otherantibodies are used to deplete cancer stem cells from a patient, forexample, from a patient's blood.

FACS and Growth of Human Stem Cells

The present invention further discloses using anti-MUC1* antibodies; orNM23 or NM23 S120G or other mutants that prefer dimerization tostimulate the growth of and inhibit the differentiation of progenitorcells that express the clipped form of MUC1 (MUC1*). Although MUC1cleavage is turned off when stem cells initiate differentiation,cleavage resumes at later stages. Hematopoietic stem cells (HSCs) forexample, express the clipped form, MUC1* and can be made to proliferateby exposing the cells to MUC1* dimerizing agents. Hematopoietic stemcells are CD34-positive and CD38-negative when they are considered stemcells. When they progress to the next stage of differentiation, theybecome CD34-positive and CD38-positive. We obtained human HSCs from cordblood and cultured them in minimal stem cell media plus anti-MUC1*antibodies at varying concentrations. Cells were cultured for 11 dayswith fresh antibodies added on day 5 post-plating. Cells were analyzedand sorted by FACS. FIGS. 16A-16E, Example 18 shows that the number ofcells that remained hematopoietic stem cells, CD34+/CD38−, increasedwith increasing anti-MUC1* concentration. Conversely, the number ofcells that had progressed to the next progenitor stage, CD34+/CD38+increased as the concentration of anti-MUC1* decreased. These resultsshow that stimulation of MUC1* growth factor receptor inhibiteddifferentiation of HSCs.

Hematopoiesis occurs in the liver of the fetus and in early life. Humanfetal liver cells were FACS sorted using an antibody that binds to thePSMGFR sequence of the MUC1* extra cellular domain and VU4H5 which is acommercially available antibody that binds to the tandem repeat units offull-length MUC1. The FACS scan of FIG. 17B shows that fetal liver cellsare mostly MUC1*-positive and full-length-negative. MUC1*-positive fetalliver cells were isolated and expanded by growing them in minimal mediaplus anti-MUC1* antibodies. The graph of FIG. 18 shows that the growthof fetal liver cells is greatly increased at optimal anti-MUC1* antibodyconcentration. The growth declines when the antibody goes to excess andthere is one antibody attached to each receptor rather than one antibodybinding to each two receptors. Similarly, undifferentiated stem cellscan be separated from those that have differentiated by performing FACSor other separation technologies using binding agents such as antibodiesthat bind to the PSMGFR region or the distal portion of the full-lengthMUC1 protein.

Other types of cells may present the clipped form of MUC1 and can beisolated or depleted from cell populations on the basis of whether ornot antibodies that recognize the PSMGFR portion of the MUC1 proteinbind to the cells.

Capture, Growth, Release, Sorting Combined

In some cases it may be desirable to separate one cell type from anotherbefore, during or after a growth period. In one method each spatialaddress of a surface presents a different ligand, each of which hasaffinity for a different cell type or for specific markers that identifya cell stage or type. Cells are added to the surface and by affinityinteraction the cells become spatially separated according to markers onthe surfaces of each cell type. Separated cells can be individuallyharvested for culturing in separate locations or can be cultured as amixture then harvested later by location. In one method, different modesof attachment are used to attach different marker-specific ligands. Forexample, at one location, ligands to MUC1*, a marker for pluripotentcells, are attached to a surface by histidine-tag/NTA-Ni interaction,while at another location, antibodies to a marker for cellsdifferentiating along the ectoderm line, are attached to the surface bya Protein G. In this way, the undifferentiated cells are released byaddition of imidzole and the ectoderm cells are released by the additionof excess Fc. In another method, the two or more surfaces that eachpresent a different affinity ligand are housed in separate locations.The two or more surfaces may be connected by flow channels. In oneembodiment, a mixture of cells is introduced to a first surface thatcaptures cells that express the cognate molecule for the ligand that thesurface presents. The supernatant or flow through is then introduced toa second surface that captures the cells that present the cognate cellsurface molecule that facilitates binding to its surface. Thesupernatant or flow through is then introduced to a third surface and soon such that the desired cell types are captured by spatiallyaddressable surfaces. This method is used to separate cells by type orto separate, then grow the cells. Flow channels and valves can be usedsuch that flow is allowed during the period of cell separation but thenlimited so that cells of a specific type can be cultured underconditions that are optimal for that particular cell type.

Methods of the invention are suitable for the separation of cells thatmay undergo differentiation during the growth process. Systems comprisedof mixed surfaces that each present an affinity ligand for a particulardifferentiation state marker or cell type are used in a dynamic systemto sort progeny as a function of differentiation state. Cells initiallyattach to a first surface by interaction of one of their cell surfaceproteins that is a marker of an initial differentiation state, which isno longer expressed by the cell or its progeny in another state ofdifferentiation. The cell would therefore be released wherein it wouldmigrate to a new location that presents a ligand with affinity for acell surface marker that defines its new differentiation state. Thissorting can take place geographically e.g. location in a flow channel,introduction of supernatant to a new surface, or self-sorting wherecells are released from one location (can be a particle) and migrate toa second location (can be a neighboring particle) where an affinityligand for a different cell marker is immobilized. In one embodiment,beads or particles that display different affinity ligands are mixedtogether and cells attach to the bead/particle for which they presentthe cognate molecule on their surface. In this case beads or particlesalso possess a property that allows them to be sorted after cellularattachment. For example, magnetic beads that present a ligand(s) withaffinity for CD34+/38− hematopoietic stem cells are mixed withnon-magnetic beads that present ligand(s) with affinity for CD34+/CD38+progenitor cells. After cell culturing, beads bearing CD34+/38− cellsare magnetically isolated and collected, while the remaining beadscomprise the population of CD34+/38+ cells. Alternatively, spatiallocations, beads or particles can have attached thereto moieties thatcan be captured by other surfaces for purification. As an example, beadsthat present an affinity ligand and a purification ligand will captureall the desired cell types via the interaction between the affinityligand and cognate cell surface receptors; the purification ligand willattach the beads to a specific spatial address via binding between thepurification ligand and a moiety on a second surface. The inventionincludes using this method to sort cells from a mixed pool wherein thecells are in various stages of differentiation. The invention alsoincludes the use of this method for sorting cells in cell culturesituations wherein cells are being induced to be pluripotent and it isdesirable to select and amplify those cells that have certain stem-likeproperties at various times during the process of inducing pluripotency.

In an alternative method, cells are separated by immobilization ontoparticles that present ligands that are specific for different celltypes. A mixture of cells is introduced to a mixture of particles. Cellsseparate onto particles that present the ligand that has affinity forits cell surface molecule. Particle-bearing cells can then be separatedprior to culturing or cultured all together then separated after agrowth period. Cell-bearing particles are separated by a variety ofmeans based on the properties of the particle itself or properties ofligands attached to the particles. For example, particles can beseparated based on size, charge, density, optical properties,electromagnetic properties and the like. These properties can beinherent properties of the particle itself or properties of an attachedligand. For example, the particles themselves may be fluorescent orligands attached to the particles may be fluorescent. Particles areeasily separated by properties including but not limited to magnetic,charged, fluorescent or electronic characteristics. Alternatively,particles can be used that present ligands that bear a second affinityligand. In this case, in addition to bearing a ligand that facilitatesthe attachment of a cell, the particle would also bear a moiety thatfacilitates the attachment of the cell-bearing particle to a separatesurface or location.

In another aspect of the invention, one surface presents two or moredifferent ligands that have different functionalities. In some cases,the two or more ligands are more selective than a single ligand for theattachment of specific cells. In another case, a first ligand mediatesthe attachment of cells while the second ligand targets the cell/surfacecomplex to a specific location that may be another surface or anotherlocation. In this way, surfaces that are articles or particles that bearligands that capture a specific cell type can be purified away fromnon-target cells via attachment to a second surface or location. Inother cases, it may be desirable to capture two or more different celltypes yet have the ability to separate the cells, according to type,either before, after or during a growth period. This is accomplished byusing surfaces or particles that present a first ligand that facilitatesattachment of a specific cell type and a second ligand that targets thesurface to a specific location. The targeting ligand may be a chemicalor biological moiety that targets the particle by binding to an entityat a different location. Alternatively, the targeting ligand may be anentity that imparts certain properties to the particle that make itseparable from other particles. For example, the ligand may be afluorescent moiety, a dye, a charged moiety, or a moiety with optical orelectromagnetic properties. In another aspect of the invention, thetargeting ligand is not a ligand per se but rather is a specificproperty of the particle.

Surfaces and novel growth factors of the invention are envisioned to beused for the growth of stem, progenitor and other MUC1*-positive cellsin a variety of formats, including but not limited to wave bags, rollerbottles, growth in suspension, and for use in any type of containmentvessel including a live host. The containment vessel may be maintainedin motion to prevent the adhesion of cells to the vessel. Theinteractions between surface-immobilized ligands and their cognatetargets on cells allow for exchange of media without loss of cells. Whenit is desired to harvest or deplete cells, surfaces which may beparticles, can be isolated by centrifugation, gravity, electromagneticor electric field. Agents can be added to release the cells from thesurfaces. Excess affinity ligands can be added free in solution so thatthey compete for binding to the receptors on the cell surface and thusrelease the cells from the particles. In one embodiment, if the affinityligand is an antibody, excess Fc portions of antibodies are added thatserve to release the antibody from the particle and cell plus activatingligand are free in solution. In another embodiment, the ligand is NM23or a mutant thereof.

The present invention further discloses using NM23 wild type or mutantsthat prefer formation of tetramers and hexamers to induce thedifferentiation of stem cells, progenitors or cells that have beeninduced to be stem-like through the introduction of nucleic acids,siRNAs, micro RNAs or proteins.

The invention also includes methods for inducing the differentiation ofstem cells and stem-like cells. Ligands that block the interaction ofMUC1* and its dimerizing ligands induce differentiation. For example,the addition of a peptide containing enough of the sequence of theextracellular domain of MUC1* to block the interaction of NM23 and MUC1*extracellular domain induces differentiation. Similarly, the addition oflow concentrations of an Fab (monovalent) of an anti-MUC1* antibodyprevents receptor dimerization, which promotes pluripotency, and resultsin initiation of differentiation. The MUC1* extra cellular domainpeptide or the Fab of antibodies that bind to MUC1* can be added toculture media or attached to surfaces. Stem cells can be harvested thenreplated over surfaces presenting ligands such as the MUC1* extracellular domain peptide of the anti-MUC1* Fab to induce differentiation.Micro RNA 145 (miR-145) suppresses MUC1 and in so doing inducesdifferentiation. miR-145 can be added to stem and progenitors in cultureto promote differentiation. In contrast, inhibitors of miR-145, such assiRNA specific for miR-145, can be added to growing stem and stem-likecells to inhibit their differentiation.

Ligand-Polymer Growth Surfaces: The attachment of ligands of theinvention to polymers or macromolecules, such as dextrin or cyclodextrangreatly improves their ability to capture and grow the targeted stem andprogenitor cells. The resultant surfaces simulate ligands in solution.The covalent attachment of both proteins and antibodies to cyclodextranincreased cellular adhesion greatly decreased the amount of ligandrequired, compared to when the ligand was directly adsorbed onto thesurface. Ligands such as NM23 or anti-MUC1* that were coupled tocyclodextran supported embryonic stem cell growth in minimal mediawithout the need for additional growth factors in the media. Antibodiesand cognate proteins like anti-MUC1* and NM23 can also be attached toother polymers and other surfaces including porous membranes andscaffolds. The invention includes both structured and un-structuredsurfaces. For example, stents, artificial structures such as ears, canbe coated with biological and/or chemical agents that facilitate theattachment of stem and progenitor cells. These ligands may optionallyprovide the stem or progenitor cells with nutrients or signals thatinfluence their growth and/or differentiation.

Synthetic Antibody Growth Surfaces: The invention also contemplates theuse of synthetic ligands as growth factors for cell growth media andalso for surface coatings that facilitate the attachment of cells. Forexample, small molecules that bind to cell surface proteins are readilyidentified using standard screening methods. The inventors previouslydisclosed small molecules that bind to the MUC1* extra cellular domain,and to the PSMGFR peptide in particular. These synthetic molecules canthen be non-covalently or covalently attached to surfaces for theadsorption and growth of non-adherent cells, such as stem cells, iPScells and early progenitors like hematopoietic stem cells that expressMUC1*. If the synthetic ligands bind to growth factor receptors that areactivated via dimerization, then activating dimers of the smallmolecules can be made by covalently linking two small molecules to makedimers. In a preferred embodiment, the small molecules bind to thePSMGFR peptide and the small molecules are linked so that they becomedimers and function as artificial growth factors. In another aspect ofthe invention, small molecule monomers can be attached to a surface sothat they are close enough together that they behave like a dimer. Thatis to say, the surface acts as the linker, so that the small moleculesare presented to the cell surface receptor in a defined geometry thatactivates the receptor. These small molecule dimers can be used in thesame ways as the natural growth factors, including that they can beadded to growth media as well as adsorbed or covalently attached tosurfaces. Synthetic surfaces would be: a) cheaper to manufacture; b)amenable to long-term storage; and c) immune to degradation. Theinventors previously described small molecules that bind to theextracellular domain of MUC1* with high affinity. Small molecule dimers(bivalent) that mimic anti-MUC1* antibodies are synthesized by couplingof the small molecules to a linker. Synthetic antibodies can beimmobilized either directly onto plate surfaces or via a polymercoating.

The present invention is not to be limited in scope by the specificembodiments described herein. Indeed, various modifications of theinvention in addition to those described herein will become apparent tothose skilled in the art from the foregoing description and accompanyingfigures. Such modifications are intended to fall within the scope of theappended claims. The following examples are offered by way ofillustration of the present invention, and not by way of limitation.

EXAMPLES Example 1. Pluripotent Stem Cells Attached to Matrigel andCultured in Minimal Media Plus Anti-MUC1* Antibodies Proliferate Fasterand with Less Differentiation than Growth Supplemented by bFGF andConditioned Media from Fibroblast Feeder Cells

H9 hESCs (WiCell) or BG01v/hOG, (Invitrogen) were cultured at 37° C. and5% CO₂ on either mitomycin-C inactivated Hs27 human foreskin fibroblasts(ATCC) in 6 well plates (BD Falcon). hESC culture media consisted ofDMEM/F12/GlutaMAX I with 20% Knockout Serum Replacement, 1%non-essential amino acids stock, 0.1 mM β-mercaptoethanol (all fromInvitrogen) and 4 ng/ml human basic fibroblastic growth factor (bFGF,Peprotech). Cells were passaged by manual dissection every 5-7 days at aratio of 1:3 and medium was changed every 48 hours. In some experiments,hESCs were grown on matrigel (BD Biosciences) with hESC culture mediasupplemented with 30% Hs27-conditioned medium and 4 ng/ml bFGF. In otherexperiments in which Anti-MUC1* was added, conditioned media and bFGFwere omitted; we refer to this as “Minimal Media”, (abbreviated MM).

FIG. 1 shows the OCT4 immunofluorescence of human stem cell coloniestreated with anti-MUC1*. H9 cells were trypsin-dissociated and seeded in8-well chamber slides pre-coated with matrigel at 4×10⁴ cells/well.Media was changed and antibodies added every other day at a finalconcentration of 1 μg/ml for bivalent anti-MUC1* for five weeks. Cellswere stained with an OCT4 specific antibody (Santa Cruz, Clones H-134and C-10) and DAPI.

FIG. 1 shows that after five (5) weeks of growth, human embryonic H9stem cells grew 100% pluripotently when cultured in minimal media plusanti-MUC1* antibodies. Cells grown identically, except that they werefed minimal media plus bFGF and 30% conditioned media from feeder cells,proliferated less and differentiated more. Compare DAPI staining ofnuclei with OCT4 staining that identifies pluripotent cells. Dottedlines mark the border of the undifferentiated portions.

Example 2. Pluripotent Stem Cells Cultured in Anti-MUC1* Over MatrigelMaintain Stable Karyotype and Differentiate Normally

BG01v/hOG hu ES cells (Invitrogen) were plated onto Matrigel andcultured in Minimal Media (see Example. 1) plus a rabbit polyclonalanti-MUC1* antibody (SRY 2a), at 80 ng/ml for 18 passages over thecourse of six (6) months. Cells were pelleted, DNA extracted andoutsourced for karyotyping. FIG. 2 shows that the karyotype at the endof 18 passages was unchanged. Note that this stem cell line hastri-somal abnormalities; however it is pertinent that the karyotype wasstable and unchanged by culturing in anti-MUC1* in the absence of othergrowth factors.

From this same batch of multiply passaged BG01v/hOG cells,undifferentiated stem cells were harvested by treatment with collagenasethen suspended in minimal media for 14 days. Note that during thisperiod, anti-MUC1* antibody is withdrawn to promote differentiation.This allowed the cells to form embryoid bodies, which were plated ontogelatin for 7 days, then stained with antibodies that recognize markersof the three germlines: FIG. 3A) Cells were OCT4-negative, indicatingthat they had differentiated; FIG. 3B) alpha fetoprotein-positive, whichis a marker for endoderm; FIG. 3C) nestin-positive, a marker forectoderm; and D) positive for smooth muscle actin, which is a marker formesoderm germline.

Example 3. Surfaces that Promote Pluripotent Stem Cell Growth

Surfaces that present a ligand that binds to and dimerizes theextracellular domain of MUC1* provide pluripotent stem cells with amethod for adhering to the plate surface and also activate the growthfactor receptor function of MUC1*. Cell culture flasks, petri dishes ormulti-well plates were coated with a rabbit polyclonal antibody raisedagainst a peptide having the sequence of the MUC1* extracellular domain:

(SEQ ID NO: 1) GTINVHDVETQFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA.Antibodies that bind to the sequence given directly above are referredto here as anti-MUC1* antibodies or anti-PSMGFR antibodies. Tissueculture treated, as well as bare plastic, and polystyrene plates wereused.

In one example, anti-MUC1* antibody (Zymed: custom antibody service) wasadded at 30, 100, or 300 ug/ml to wells of a 96-well cell culturetreated plate (Tissue Culture Test Plate 96F TPP #92096) and allowed toadsorb overnight at 4 degrees C. Undifferentiated BG01v/hOG (Invitrogen)stem cells were suspended in Minimal Media. Minimal Media is 400 mlDME/F12/GlutaMAX I (Invitrogen #10565-018; 100 ml Knockout SerumReplacement (KO-SR, Invitrogen #10828-028); and 5 ml 100×MEMNon-essential Amino Acid Solution (Invitrogen #11140-050); and 0.9 ml(0.1 mM) β-mercaptoethanol (55 mM stock, Invitrogen #21985-023). TheBG01v/hOG stem cells were plated onto anti-MUC1* antibody coatedsurfaces at a density of 10,000 cells per well. Cells were allowed toadhere for 24 hrs. Cells were then cultured in Minimal Media alone for 5days, with media changed every 48 hours.

For comparison, cells in control wells were cultured in mediasupplemented with 4 ng/ml of bFGF and 30% conditioned media from HS27fibroblasts. FIG. 4 shows the graph from a Calcein-AM (Molecular Probes)staining, in which fluorescence from live cells is measured as afunction of anti-MUC1* antibody density on the surface that those cellswere grown. The graph of FIG. 4 shows that cells grown on anti-MUC1*surfaces proliferate in the absence of any other growth factors. Growthis only moderately enhanced by the addition of bFGF and uncharacterizedfactors secreted from feeder cells. As a negative control, an irrelevantantibody was plated onto surfaces. Stem cells that were plated ontothese surfaces did not adhere and were either floating or dead by theend of the 24-hour attachment period.

In parallel, the resultant stem cells were double stained with DAPI(nuclear stain) and anti-OCT4. The 1:1 correlation of OCT4 positivityand DAPI staining confirms that the resulting cells were pluripotent,see FIGS. 5A-5D.

Example 4. Human Pluripotent Stem Cells Proliferate on Anti-MUC1*Antibody Surfaces with or without MUC1* Stimulators Added into Solution

Human embryonic stem cell lines were tested for their ability to grow onanti-MUC1* antibody adsorbed to either tissue culture treated plates,polystyrene plates, or chamber slide plates. Anti-MUC1* at 100 ug/ml wasadsorbed onto the plates and allowed to adsorb at 4 degrees C.overnight. Undifferentiated human H9 embryonic stem cells were plated ateither 10,000 cells or 40,000 cells per well of a 96-well or at 25,000cells per well of 8-well plates. In all cases, undifferentiated stemcells attached and proliferated on anti-MUC1* surfaces, cultured inminimal media alone or with anti-MUC1* added into minimal stem cellgrowth media. The undifferentiated H9 stem cells were then cultured in:A) Minimal Media; B) minimal media plus anti-MUC1* antibody at 80 ng/ml;or C) minimal media plus bFGF at 4 ng/ml and 50% conditioned media frominactivated HS27 fibroblast feeder cells. Experiments were performed intriplicate. Undifferentiated stem cells adhered to anti-MUC1* surfaces.Undifferentiated colonies grew fastest when anti-MUC1* antibody was alsoadded into minimal media. However, undifferentiated stem cell coloniesof similar morphology and quality developed a day or two later in wellsthat were cultured in minimal media alone. The amount of proliferationand quality of undifferentiated stem cell colonies were comparablewhether cells were cultured in minimal media, minimal media plusanti-MUC1* or plus bFGF and conditioned media from fibroblasts.Pluripotent stem cells resulted and could be split between days 5 and 7,which is typical for stem cells grown according to standard feeder cell,bFGF protocols. FIG. 6 shows photos of wells grown when cultured indifferent media. FIGS. 6G and 6H) minimal media; FIGS. 6E and 6F)minimal media plus anti-MUC1* antibody at 80 ng/ml; or FIGS. 6C and 6D)minimal media plus bFGF at 4 ng/ml and 50% conditioned media fromfibroblast feeder cells. Panels on the left (e.g. 6C, 6E, 6G) are photostaken after 3 days of growth. Panels on the right (e.g., 6D, 6F, and 6Hare photos of the same wells taken at day 7.

Example 5. Method for Harvesting Stem Cells

The stem cells grown in Example 4 above were ready for harvesting andsplitting at day 7. Since cells were immobilized on an anti-MUC1*surface, we reasoned that they could be released by adding a peptidethat would compete with the cell surface receptor for binding to theanti-MUC1* antibody on the plate surface. The peptide having thesequence

(SEQ ID NO: 1) GTINVHDVETQFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA,corresponds to the extracellular domain of the MUC1* receptor and wasalso the peptide that the anti-MUC1* antibody was raised against, isreferred to here as the MUC1*_(ecd) peptide or PSMGFR peptide. TheMUC1*_(ecd) peptide was added to the growing stem cells at aconcentration of 10 uM and incubated for 30 minutes. At that time, itwas observed that the stem cells had been released from the surface.Stem cells were collected in the supernatant, rinsed and re-plated ontofresh anti-MUC1* surfaces, where cells adhered and continued toproliferate. This procedure was also successfully performed using humanembryonic stem (huES) cell line BG01v/hOG (Invitrogen), then huES H9s.FIGS. 6A and 6B shows H9 stem cells that were grown on anti-MUC1*antibody surfaces, cultured from single cells, then harvested bycompetitive peptide release, and re-plated onto fresh anti-MUC1*surfaces where they continued to proliferate.

Example 6. Anti-MUC1* Antibody Coupled to Beta-Cyclodextrin StimulatesSolution Interaction of MUC1* Growth Factor with Cell Surface Receptors

Anti-MUC1* antibodies were covalently coupled to carboxy-β-cyclodextrin(Cβ-CD) according to a standard coupling protocol (Fraschini, C.;Vignon, M. R. Selective oxidation of primary alcohol groups ofβ-cyclodextrin mediated by 2,2,6,6-tetramethylpiperidine-1-oxyl radical(TEMPO). Carbohydrate Research 2000. 328(4):585-589). 96-well cellculture treated plates (Tissue Culture Test Plate 96F TPP #92096) werecoated with anti-MUC1* coupled to beta-cyclodextrin, at 0, 10, 30, 100,300, or 1000 ug/ml final antibody concentration; the concentration ofbeta-cyclodextrin in each well was kept constant with only theconcentration of the antibody varied. As a control, anti-MUC1*antibodies were directly adsorbed onto the plates without cyclodextrin.Single cell suspensions of BG01v/hOG stem cells were made, and cellswere plated at a density of 10,000 cells/well in minimal medium. Stemcells attached to, and proliferated on both the antibody surfaces andantibody coupled to cyclodextrin surfaces. No other growth factors wereadded. Two days post-plating, live cells were assayed by Calcein-AMreagent. The graph of FIG. 7 shows that stem cell growth in minimalmedia is supported by anti-MUC1* antibodies presented on betacyclodextrin and that the amount of antibody required is less than nakedantibody adsorbed onto the growth plate, perhaps because of the3-dimensional presentation of the antibody to the growing cells.

Example 7. Antibodies Against any Cell Surface Antigen Will Allow StemCells to Attach to a Surface and Will Proliferate if Cultured byConventional Means or by Adding Anti-MUC1* Antibody to Minimal Media

SSEA4, Tra 1-60, and Tra 1-81 antibodies promote pluripotent stem cellgrowth when cultured in minimal media plus anti-MUC1* antibody. 96-wellcell culture treated plates (Tissue Culture Test Plate 96F TPP #92096)plates were separately coated in triplicate at 4° C. with Anti-SSEA4(Santa Cruz), Anti-Tra 1-60 (Santa Cruz), or Anti-Tra 1-81 (Santa Cruz)antibodies at final concentrations of 0, 3, 10, 30, and 100 ug/ml insterile PBS. The following day, cells were rinsed with PBS. BG01v/hOGhuman embryonic stem cells (Invitrogen) that had been grown on matrigeland cultured in minimal stem cell growth media plus 30% conditionedmedia from fibroblasts plus 4 ng/ml bFGF were used to make single cellsuspensions. Cells were plated in each well at a density of 10,000 cellsper well in Minimal Media. The following day, medium was removed fromwells, and replaced with Minimal Media plus 80 ng/ml Anti-MUC1*antibody. Media was changed every other day, and cells were assayed byCalcein-AM reagent. FIG. 8 shows that stem cells can attach to a surfacevia interaction with a cell surface protein and its cognate antibody,then can be cultured in minimal media plus anti-MUC1* antibody or withany standard stem cell growth media.

Similarly, H9 undifferentiated stem cells were plated at a density of10,000 cells per well of a 96-well plate onto which anti-SSEA4antibodies had previously been adsorbed (100 ug/ml). The stem cells werecultured for eight (8) days in minimal stem cell growth media plusanti-MUC1* antibody at 80 ng/ml. Undifferentiated stem cell coloniesdeveloped and proliferated.

Experiments were performed in parallel that showed that H9 humanembryonic stem cells bound to anti-SSEA4 and anti-Tra 1-81 that had beenadsorbed onto the surface of 96-well and 12-well plates. Cells were thencultured in either standard stem cell growth media containing bFGF at 4ng/ml and 50% conditioned media from HS27 fibroblast feeder cells, or inminimal media plus anti-MUC1* antibodies at 80 ng/ml, or in minimalmedia plus recombinant NM23-S120G at 8 nM. Undifferentiated stem cellcolonies formed in all cases that were morphologically identical stemcell colonies grown by standard methods. When either an irrelevantantibody replaced anti-MUC1* antibodies, or cells were cultured inminimal media alone, stem cells died within about a day.

Example 8. Addition of MUC1*_(ecd) Peptide Induces Differentiation

Undifferentiated human stem cells growing on either feeder cells,matrigel or growth surfaces can be rapidly induced to differentiate bythe addition of the MUC1*_(ecd) peptide. The peptide competes with thenatural ligand for binding to the MUC1* growth factor receptor; theinteraction of the natural ligand with MUC1* promotes pluripotent cellgrowth. Blocking this interaction inhibits the pluripotent stem cellgrowth and induces cells to differentiate. H9 stem cells growing onmatrigel differentiated about three times faster after treatment withthe MUC1*_(ecd) peptide. The MUC1* extra cellular domain peptide can beused to harvest stem cells from surfaces coated with ligands of MUC1*.Increased rates of differentiation were prevented by incubating theharvested cells with either anti-MUC1* to compete away the peptide,followed by rinsing and re-plating.

Example 9. NM23 in Minimal Media is Equivalent to State of the Art bFGFPlus Conditioned Media from HS27 Fibroblast Feeder Cells for the Cultureof Human Stem Cells

Undifferentiated H9 human embryonic stem cells were harvested by manualdissection. Colony pieces, approximately 0.1 cm on edge, were mixed intominimal media and uniformly distributed onto 24-well plates that hadbeen coated with stem cell quality matrigel according to themanufacturer's directions. Undifferentiated colonies pieces from (3)wells of a 6-well plate were transferred to a 24-well plate. RecombinantNM23-S120G (mutant that preferentially forms dimers) at either 4 nM or 8nM concentration in minimal media (MM) was compared to the state of theart, which is currently 4 ng/ml bFGF (basic fibroblast growth factor)plus 50% conditioned media (CM) from inactivated HS27 fibroblast feedercells. We also tested the effect of treating the freshly plated cellswith bFGF/CM for the first 24 hours then switching to the NM23 in MM.After 4 days in culture, the numbers of undifferentiated versusdifferentiated colonies were counted. The results are graphed in FIG. 9.The bars marked CONTROL refer to the standard method of culturing overmatrigel in 4 ng/ml bFGF and 50% CM from inactivated HS27 fibroblastfeeder cells. The graph shows that: 1) cells growing in NM23+MM grewfaster than bFGF+CM; 2) NM23+MM had less differentiation than the stateof the art; 3) adding bFGF+CM for the first 24 hours was slightly worsethan directly culturing in NM23+MM; and 4) the trend appears to indicatethat the highest concentration of NM23 (8 nM) was best.

Cells were split on day 5 and re-plated over matrigel. For the next 5days, cells were cultured in either 4, 8, 16, 32 or 64 nM. Resultsshowed that increased concentrations of NM23-S120G worked better. 16 nMand 32 nM NM23-S120G produced roughly the same number and quality ofundifferentiated colonies as the bFGF+CM control. At 16 nM, each wellyielded 4-5 colonies where only 1 was differentiated; 32 nM wells eachyielded 3 colonies total with 1 partially differentiated; bFGF+CMcontrols produced 2 undifferentiated colonies and 1 partiallydifferentiated in one well and 1 undifferentiated, 2 fullydifferentiated in the other well. NM23-S120G produced much largercolonies than bFGF/CM.

Example 10. Anti-MUC1* Coupled to Cyclodextran Plus Anti-MUC1*orbFGF-Anti-MUC1* Antibodies Coupled to Cyclodextran Promote Stem CellAttachment and Growth in Either Traditional Media or Minimal Media PlusMUC1* Stimulators

Human embryonic H9 stem cells that had been growing by standard methodson HS27 fibroblasts, then on matrigel for 2 passages were manuallydissected and harvested as described in Example 9. Undifferentiatedcolony pieces from 2 wells of a 6-well plate were passaged onto wells ofa 24-well plate that were coated with anti-MUC1* antibody covalentlycoupled to cyclodextran. Cells were then cultured in either anti-MUC1*antibody in Minimal Media at a final concentration of 160 ng/ml or 4ng/ml bFGF and 50% HS27 conditioned media (CM). Cells attached withinhours grew as one would expect for growth over feeder cells or matrigel,except with an accelerated growth rate. Cells were ready to be split atbetween day 5 and 6 post plating. Undifferentiated colony pieces weremanually harvested and re-plated onto new cyclodextran-anti-MUC1* coatedplates where they continued to proliferate and form undifferentiatedcolonies. Cell number, colony morphology and inhibition ofdifferentiation were comparable between wells cultured in anti-MUC1* andbFGF plus HS27 CM.

Example 11. Method for Coupling Ligands to Cyclodextran

Dextran Carboxylation: Materials: Dextran 500 (Avg. MW is 500 kD,Aldrich cat. #31392, isolated from Leuconostoc spp., Sigma-Aldrich, St.Louis, Mo.); Bromoacetic Acid and NaOH (Sigma-Aldrich); Type I H₂O(Ricca Chemical Company, Arlington, Tex.); 20,000 MWCO dialysis tubing,or slides (Fisher Scientific, Waltham, Mass.).

Procedure: A 2N solution of NaOH was prepared with Type I H₂O. Into aclean, dry 20 mL scintillation vial was added 6 mL of the abovesolution. To this was added 834 mg of bromoacetic acid, solution becamecloudy after dissolution. Then 1.00 g of Dextran 500 was added to thevial and the solution was subjected to vortexing and lightultrasonication to give complete dissolution within 5 minutes. Thissolution was then stirred at room temperature for 24 hours. Solution wasthen dialyzed against running tap water for 8 h, then dialyzed against0.1 N HCl for 18 h, then dialyzed against distilled water for 12 hours.Solution then freeze-dried and stored under argon at −20° C.

Dextran-Protein/Antibody Coupling: Materials: Carboxylated Dextran 500,prepared in-house; 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC)(Sigma-Aldrich); N-Hydroxysuccinimide (NHS) (Sigma-Aldrich); Protein orantibody to be coupled; Type I H₂O (Ricca Chemical Company);Ethanolamine (Sigma-Aldrich).

Procedure: A solution of 0.5 mg/mL carboxylated dextran 500 in Type IH₂O was prepared. A solution of 100 mM EDC/100 mM NHS in Type I H₂O wasprepared. In a 1.5 mL eppendorf tube, an aliquot 1 mL of the dextransolution was added to 12 μL of the EDC/NHS solution. The mixture wasvortexed, and allowed to rock at room temperature for 15 minutes toactivate the carboxylic acid residues. Meanwhile, 6.67 nmol of proteinor antibody (dissolved in an appropriate buffer) was aliquoted into aseparate tube. After the 15 minute activation, 110 μL of the activateddextran solution was pipeted into the tube containing the protein orantibody to be coupled. The solution was gently vortexed to mix, thenlightly rocked tube at room temperature for 2 h. 5 μL of ethanolaminewas added into the tube and allowed to rock for an additional 15 minutesat room temperature. The contents of the tube were dialyzed againstphosphate buffered saline (pH 7.4) at 4° C. for at least 18 hours. Thesolution may be used fresh or can be lyophilized, stored at −20° C., andsubsequently reconstituted prior to use.

Note that we empirically determined the optimal amounts of carboxylationand concentrations of protein to be coupled by testing the growth ofstem cells on 24 surfaces in which carboxylation and proteinconcentration were systematically varied.

Example 12. H9 Stem Cells Attached to Anti-MUC1* Coupled to Cyclodextranand Cultured in Either NM23-S120G in Minimal Media or bFGF in HS27Conditioned Media

24 well plates were coated with anti-MUC1* coupled to cyclodextran, asdescribed in Example 11. H9 cells were passaged onto these surfaces asdescribed in Example 9 and cultured in recombinant NM23-S120G in minimalmedia at a final concentration of 1 nM, 2 nM, 4 nM, or 8 nM. In anothercondition, cells were treated with 4 ng/ml bFGF and 50% HS27 conditionedmedia (CM) for 24 hours before being switched to Nm23-S120G in minimalmedia. Experiments were performed in duplicate. After 4 days growth, thenumber of undifferentiated versus differentiated colonies were countedand graphed as percentage undifferentiated colonies to the total numberof colonies. Only colonies that were 100% undifferentiated were countedas undifferentiated. FIG. 10 shows that bFGF plus CM is only helpfulwhen the concentration of NM23-S120G is insufficient. Further, resultsshowed that NM23-S120G in minimal media performed as well or better thanbFGF plus fibroblast feeder cell conditioned media, in terms of colonymorphology, number and inhibition of differentiation.

Example 13. Procedure for Coating Culture Flasks with NTA-Ni

Materials: 24-well carboxylic-acid-presenting-surface cell-culture plate(BD Biosciences Purecoat: #356775); 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC); N-Hydroxysuccinimide (NHS);N_(α),N_(α)-Bis(carboxymethyl)-L-lysine Hydrate; Type I H₂O; Sterilesyringe (20 mL); 0.45 μm PVDF-membrane syringe filters.

Procedure: 75 mL of 10 mM EDC/10 mM NHS solution per plate to bederivatized was prepared. Using a sterile syringe and syringe filter,the EDC/NHS solution was filtered into each well, filling the wells˜80%. Plates were covered and shaken gently on a plate-shaker at roomtemperature for 15 minutes. While the plates were shaking, ˜40 mL of 10mM N_(α),N_(α)-bis(carboxymethyl)-L-lysine hydrate per plate wereprepared. After the 15 minutes activation of the plates, the plates wereemptied and rinsed 3× with Type I water. Using a fresh sterile syringeand syringe filter, the solution ofN_(α),N_(α)-bis(carboxymethyl)-L-lysine hydrate were filtered into eachwell, filling the wells about halfway. The plates were covered andshaken gently at room temperature for 3 hours. After 3 hours, the plateswere emptied and rinsed 5× with Type I water. Remaining activatedNETS-esters were quenched at this point by adding a sterile solution of1% ethanolamine and incubating at room temperature for 15 minutes, thenadding a sterile solution of 10% sodium carbonate and incubating at roomtemperature for 30 minutes. This can also be accomplished by storing theplates in sterile, Type I H₂O for at least 48-72 hours at 4° C. Onceresidual NHS esters have been either quenched or hydrolyzed back to thecarboxylic acids, wells must be filled with sterile, Type I H₂O, thenwrapped in parafilm, covered, wrapped in tin foil, and stored at 4° C.Plates should be rinsed again with sterile, Type 1 H₂O immediately priorto use. A 1% nickel sulfate solution was added to the plates, thenrinsed with PBS prior to use.

Note that the use of the ethanolamine solution will convert the residualNHS esters into amides presenting a hydroxyl head group. This will alterthe surface chemistry. If this is not desirable, use of either thecarbonate-solution soak or long-term-aqueous soak will hydrolyze allremaining NHS esters back to the original carboxylic acids.

Example 14. H9 Stem Cells Attached to NTA-Ni Plates that were Coatedwith Ligands Bearing Histidine Tags

12-well plates were derivatized with NTA-Ni as described in Example 13.Histidine tagged NM23-S120G, a synthetic peptide of sequenceHHHHHHSSSSGSSSSGSSSSGGRGDSGRGDS (SEQ ID NO:5) (RGD peptide), andrecombinant, histidine tagged Protein G (Minerva) were separately addedto NTA-Ni coated wells at a final concentration of 200 nM and incubatedfor 15 minutes. Plates were rinsed in PBS. To the Protein G wells,anti-SSEA4 and anti-Tra 1-81 were added at 200 nM and incubated for 15minutes, then washed with PBS. Colony pieces were harvested as describedin Example 9 from 3 wells of a 6-well plate of H9 cells growing overmatrigel for 2 passages were plated onto the wells. The stem cells werecultured in either 8 nM NM23-S120G in minimal media, 4 ng/ml bFGF plusHS27 CM, 8 nM NM23-S120G plus 50% conditioned media collected from T47DMUC1*-positive cancer cells (“Ca CM”), or 4 ng/ml bFGF plus 50% Ca CM.Cells attached to the plates within 24 hours and undifferentiated stemcell proliferation was observed. On Day 3 post plating, undifferentiatedand differentiating colonies were counted and plotted, See FIG. 11A.Representative photos (40×) were taken of: FIG. 11B) NM23-S120G surfaceand cultured in 8 nM NM23-S120G plus 50% Ca CM; FIG. 11C) RGD peptidesurface and cultured in 8 nM NM23-S120G plus 50% Ca CM; FIG. 11D) RGDpeptide surface and cultured in 4 ng/ml bFGF plus 50% HS27 CM; FIG. 11E)Protein G surface, anti-SSEA4 then cultured in 8 nM NM23-S120G plus 50%Ca CM; FIG. 11F) Protein G surface, anti-Tra 1-81 then cultured in 8 nMNM23-S120G plus 50% Ca CM; FIG. 11G) RGD peptide surface and cultured in4 ng/ml bFGF plus 50% Ca CM. The best conditions for this experimentwere obtained from His-tagged Protein G attached to the NTA-Ni surface,then affinity attached to anti-SSEA4 or Tra 1-81, then cultured inNM23-S120G in MM or CaCM.

In similar experiments, conditioned media from other MUC1*-positivecancer cells (ZR-75-1 and ZR-75-30) was used and produced the sameresults.

Example 15. Conditioned Media Collected from MUC1*-Positive Cancer CellsPromotes Stem Cell Growth and Inhibits Differentiation Better thanConditioned Media from Fibroblasts

Human embryonic stem cells (H9s) were grown according to standardmethods on matrigel in 6-well plates then harvested by manualdissection. Colony pieces from (3) wells of the 6-well plate weredistributed over the wells of a 24-well NTA-Ni coated plate. We werecurious to see if proteins on the cell surface or proteins in the mediawould adhere to the metal chelate attached to the plate surface. Themedia that was added to the plated colony pieces was either: a) 4 ng/mlbFGF plus HS27 (fibroblast) conditioned media (CM); b) 4 ng/ml bFGF plusconditioned media from T47Ds (a MUC1* positive breast cancer cell line,CM from these cells referred to here as “Ca CM”); c) 4 nM NM23 inminimal media (“MM”); d) 8 nM NM23 in MA/I; e) 4 nM NM23 in Ca CM; or f)8 nM NM23 in Ca CM. After 24 hours, it was observed that cells in eitherminimal or CM or Ca CM had attached to the surface, even though therewas no obvious reason why cells in bFGF/CM or bFGF Ca CM should attach;recall that NM23 that we used was a histidine-tagged recombinant proteinthat would be readily captured by the NTA-Ni plate. It was observed thatcells growing in the cancer cell conditioned media, Ca CM, were growingmuch better than the other conditions. After 6 in days in culture, withmedia change every 48 hours, the plates were analyzed for stem cellcolony morphology, numbers of colonies and degree of differentiation.Stem cells cultured in 4 ng/ml bFGF plus cancer cell conditioned mediaformed many more colonies and had much less differentiation (none) thanthe control of bFGF plus HS27. Cells cultured in NM23 alone grew andformed colonies, but cells cultured in NM23 plus cancer cell conditionedmedia formed more colonies than any other condition and the colonieswere about 80-85% undifferentiated and fully formed and ready to besplit, whereas state of the art methods on feeder cells or matrigelwould take 9 days to reach the same stage, albeit with 30-40%differentiation on average. FIG. 12 shows a graph of colony number atday 9; NM23 plus cancer cell conditioned media (Ca CM) we have graphedat 20 colonies but the cells had completely covered the entire well andcould not actually be counted. At day 9, there were stillundifferentiated portions roughly equal to the percentage of the controlbFGF plus HS27 fibroblast conditioned media (HS27CM), although in theNM23 stimulated wells, cells proliferated much faster.

Example 16. Antibodies that Bind to Peptide Regions that are Distal tothe Cell Surface are Preferred for Cellular Adhesion

Antibodies that bind to portions of the MUC1* extra cellular domain thatare distal to the cell surface are better for facilitating stem celladhesion than antibodies that bind to regions close to the cell surface.The extra cellular domain of MUC1* is about 45 amino acids in length.Polyclonal antibodies that were raised against the 45 amino acidpeptide, referred to here and in previous applications as PSMGFR havingthe sequence

(SEQ ID NO: 1) GTINVHDVETQFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGAfacilitated stem cell adhesion to surfaces to which they were attached.A screen of monoclonal antibodies showed that those that recognizedportions of MUC1* extra cellular domain close to the cell surface didnot promote stem cell adhesion to surfaces even though those samemonoclonals stimulated stem cell growth when added into the media. Toidentify hybridomas that produced antibodies that bound to distalportions of the MUC1* receptor, we adsorbed hybridoma supernatants ontothe wells of a 96-well plate, then plated undifferentiated colony piecesharvested from BG01v/hOG cells growing on Matrigel. Supernatants fromthree (3) clones enabled stem cell adhesion. Minimal Media was changedevery 48 hours and proliferating undifferentiated stem cell colonieswere photographed on day 9 post plating, see FIGS. 13A-13C.

In a follow up experiment, an ELISA assay was performed to determine ifthe antibodies secreted by these hybridomas did in fact bind to thedistal portion of the MUC1* extra cellular domain, see FIG. 14. Twodeletion peptides were synthesized: one missing the 10 N-terminal aminoacids, N-10 PSMGFR, with a sequence QFNQYKTEAASRYNLTISDVSVSDVPFPFSAQSGA(SEQ ID NO:3); and one missing 10 amino acids at the C-terminal end,C-10 PSMGFR having a sequence GTINVHDVETQFNQYKTEAASRYNLTISDVSVSDV (SEQID NO:4). The hybridoma supernatants that caused stem cell adhesion tothe wells of the 96-well plate, were those that by ELISA assay wereshown to bind to the peptide missing the 10 amino acids proximal to thecell surface, but not to the peptide that was missing the distal 10amino acids. Stem cells plated on the hybridoma supernatants grew intofully formed colonies that were undifferentiated after days of culturein minimal media alone.

Example 17. MUC1* Antibodies are Used to Identify Pluripotent Stem Cellsfrom Differentiating Ones

The MUC1* ligand, NM23, co-localizes with MUC1* and OCT4 onundifferentiated hESCs but immuno-reactivity of all three proteins islost in the portion of the colony that has begun to differentiate.Undifferentiated H9 hESC colonies stained positive for NM23, MUC1* andOCT4. Newly differentiating colonies did not react with antibodiesagainst any of the three proteins. Co-expression of NM23 with OCT4 andMUC1* is best seen in colonies that have begun to differentiate. Thedotted line marks the border between undifferentiated and differentiatedportions of the colonies. Triple staining experiments were performedusing: FIG. 15G) anti-NM23 (green). FIG. 15H) Anti-MUC1* (red). FIG.15I). anti-NM23 (green), anti-MUC1* (red) and DAPI (blue). A similarcolony was stained with: FIG. 15J) anti-NM23 (green). FIG. 15K)anti-OCT4 (red). FIG. 15L) anti-NM23 (green), anti-OCT4 (red) and DAPI(blue). Scale bar=100 μm. Anti-NM23 was purchased from Santa Cruz, CloneNM301 and BD Biosciences, Clone 56. Anti-MUC1* was custom generated froma Minerva PSMGFR peptide by Zymed.

Pluripotent stem cells can be isolated from mixed pools ofundifferentiated and differentiated stem cells by labeling live cellswith Anti-MUC1* and an antibody such as VU4H5 that binds to full-lengthMUC1, then sorting by FACS, magnetic cell separation or similartechnologies. MUC1*-positivity denotes pluripotent stem cells. Bivalentanti-MUC1* bound to live cells does not interfere with subsequent growthbecause it functions as a growth factor, so is ideal for cellseparations.

Example 18. MUC1* Antibodies are Used to Isolate MUC1* Early ProgenitorsAway from Later Stage Progenitors—Hematopoietic Stem Cells

CD34-positive hematopoietic stem cells (HSCs) obtained from human cordblood (ALLCELLS) were obtained. The cells contained a mixture ofCD34+/CD38−, reported to be true HSCs, but also contained CD34+/CD38+(the next progenitor stage). Cells were defrosted, pelleted, washed inSFEM (Serum-Free Expansion Medium) from StemSpan, and resuspended withSFEM with no growth factors added. Approximately 4000 cells were platedin wells of a 96 well plate covered with poly-HEMA to prevent adhesion.Rabbit polyclonal Anti-MUC1* antibody, generated by immunizing with thePSMGFR peptide, was added to each of 5 wells to a final concentration of0, 80, 250, and 2000 ng/ml. Cells were photographed at Day 3, FIGS. 16A-16D. Day 5 post plating, antibody was re-added to cells.

11 days post plating, cells were visually inspected and most were stillthe same diameter as they were when plated, which is an indicator thatthey were still hematopoietic stem cells and had not progressed to thenext progenitor stage. Cells from identical wells were pooled, andstained with anti-CD34-FITC and anti-CD38-PE-Cy5. Cells were analyzedand sorted by FACS (fluorescence activated cell sorting). FIG. 16 Eshows that as the concentration of MUC1* antibody is increased, thepercentage of cells that remained true hematopoietic stem cells(CD34+/CD38−) increased. The converse was true as well. The percentageof cells that had progressed to the next progenitor stage (CD34+/CD38+)was the highest when the concentration of MUC1* antibody was the lowest.Statistics from representative wells show that stimulation with MUC1*antibody results in more CD34+/38− cells (HSC) and fewer CD34+/38+(progenitor) cells than unstimulated cells.

Example 19. FACS Sorting of Fetal Liver Cells and Subsequent Growth byMUC1* Stimulation

FACS analysis using antibodies that recognized either full-length MUC1(VU4H5, Santa Cruz Biotechnology; or HMPV, BD Biosciences) or anti-MUC1*(rabbit polyclonal from PSMGFR immunization, Minerva) was performed on anumber of different progenitor cells to determine which expressed MUC1*,so that those cells could be isolated and expanded by stimulating theMUC1* receptor. FIG. 17 A shows that neural stem cells (RenCell CXMillipore) express MUC1*. A small number of cells express both cleavedand uncleaved MUC1. Their growth is stimulated by culturing withanti-MUC1* or other agents like NM23 that dimerize MUC1*. Fetal livercells (ALLCELLS) almost exclusively express MUC1*, FIG. 17 B.

Fetal liver cells were cultured in Minimal Media plus anti-MUC1*antibody at the concentrations indicated in FIG. 18. The growth curveshown shows that the growth of these MUC1* progenitors is stimulated bydimerization of the MUC1* growth factor receptor. At optimal antibodyconcentration, one antibody dimerizes two MUC1* receptors and when theantibody goes to excess, there is one antibody per receptor and thegrowth is inhibited. These results show that hematopoietic stem cells aswell as other progenitor cells that express MUC1* can be expanded addingagents that dimerize the MUC1* receptor.

Example 20. Hu ES Cells Adhere to Surfaces Coated with Antibody Againstany Cell Surface Marker Protein and can be Cultured in Either StandardStem Cell Media or in Media Containing MUC1* Stimulators

12-well plates were coated with 0.5 ml of either anti-MUC1* oranti-SSEA4 antibody at a concentration of 100 ug/ml. Plates wereincubated overnight at 4 degrees C., then rinsed in sterile PBS.Undifferentiated colony pieces from hu ES H9 cells growing on Matrigelwere manually dissected, resuspended, then plated over the surfaces.Media was added that contained either a recombinant NM23-S120G (Minerva)at 8 nM final concentration or 4 ng/ml bFGF plus 50% HS27 fibroblastconditioned media. Undifferentiated colonies were manually harvested onday 5 post plating, split and re-plated onto identically coatedsurfaces. The graph of FIG. 19 shows that stem cells grow on eitherantibody surfaces if cultured in NM23 in Minimal media (MM) or bFGF plusHS27 conditioned media. It was noted that cells in NM23 treated wellsgrew considerably faster than in the bFGF treated wells.

Example 21. Identification of Agents in Cancer Cell Conditioned Mediathat Promote Stem Cell Growth and Inhibit Differentiation

Conditioned media from MUC1*-positive cancer cells promotes the growthof human stem cells while inhibiting their differentiation. It would bedesirable to identify discrete agents in the cancer conditioned mediathat affect the growth of stem cells for two reasons. First, theseagents could be made synthetically or recombinantly and added asdiscrete agents to growth media or surface coatings to promote thegrowth of stem cells and certain early progenitors. Secondly,identification of those agents would enable strategies to suppress themfor the treatment of cancers.

To identify proteins in the cancer cell conditioned media Ca CM, onewould collect the Ca CM from MUC1*-positive cancer cells and separateout its individual components by, for example, separation on a column,such as ion exchange, size exclusion and the like. The various fractionswould be separately, or in combinations, tested for their ability tostimulate undifferentiated stem cell growth. The fraction(s) thatimparted the effect would then be analyzed by micro sequencing or massspec to determine the identity of the components.

A more directed approach is to compare the Ca CM from untreatedMUC1*-positive cancer cells to that collected from cells treated withmiR-145. miR-145 is a regulatory micro RNA whose expression isupregulated when stem cells transition from undifferentiated todifferentiated. Recall that during this transition, MUC1 cleavage ceasesand MUC1 expression is down regulated. It has recently been shown thatmiR-145 silences MUC1. Treating cancer cells with miR-145 will cause ashift to regulated growth characteristic of differentiation rather thanthe stem-like growth characteristic of both cancer cell growth and thatof undifferentiated stem cells. Comparison of factors secreted by naivecancer cells and those treated with miR-145 would identify those agentsresponsible for promoting stem cell and cancer cell growth. They wouldbe present in the untreated Ca CM and absent from the treated Ca CM.Identification could be accomplished by the same sort of proteinseparation then sequencing or mass spec analysis. Components could beseparated on a gel, protein bands unique to the untreated Ca CM would beexcised from the gel then analyzed by micro sequencing or mass spec.

In parallel, conditioned media from undifferentiated stem cells would becompared to conditioned media collected from stem cells treated with anagent that initiates differentiation, such as the MUC1* extra cellulardomain peptide. In this case, the components uniquely or preferentiallysecreted by the untreated stem cells would be those desirable as agentsto promote stem cell growth or induce pluripotency. Molecules thatsuppress these agents would be used as cancer therapeutics. In contrast,those components uniquely or preferentially secreted by thedifferentiating stem cells would be desirable as agents to treat cancer.Similarly, molecules that suppress these agents would be used to promotethe growth of stem cells or to induce pluripotency.

Regulatory nucleic acids, such as micro RNAs, that either promote orsuppress stem-like growth, i.e. stem or cancer cell growth, would beidentified as described above with the exception that rather thananalyzing secretions from the cells, the nucleic acids would beextracted and analyzed. For example, the technique known as DeepSequencing and total transcriptome analyses can be performed to identifythose regulatory RNAs that are either up- or down-regulated whenstem-like growth is suppressed. Regulatory RNAs that are upregulatedwhen stem cells differentiate such as miR-145 could be used asanti-cancer treatments. Similarly, molecules including siRNAs thatsuppress these micro RNAs can be used to promote or induce pluripotency.Regulatory nucleic acids that are upregulated in undifferentiated stemcell growth and cancer cell growth would be targeted for silencing orsuppression in treatments of cancer or to synchronize initiation ofdifferentiation of stem cells.

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention specifically described herein. Suchequivalents are intended to be encompassed in the scope of the claims.

1-48. (canceled)
 49. A method for promoting surface adhesion of a stemor stem-like cell, the method comprising contacting the stem orstem-like cell with an antibody that preferentially binds to a distalportion of Primary Sequence of the MUC1 Growth Factor Receptor (PSMGFR)over a proximal portion of PSMGFR, wherein the distal portion of PSMGFRcomprises the amino acid sequence of SEQ ID NO. 4 (C-10), and whereinthe proximal portion of PSMGFR comprises the amino acid sequence of SEQID NO. 3 (N-10), thereby promoting surface adhesion of the stem orstem-like cell.
 50. The method of claim 49, wherein the antibody doesnot specifically bind to SEQ ID NO. 3 (N-10).
 51. The method of claim49, wherein the method promotes surface adhesion of the stem orstem-like cell to a greater extent as compared to a correspondingantibody generated against the full PSMGFR peptide.
 52. The method ofclaim 49, wherein the method promotes surface adhesion of the stem orstem-like cell to a greater extent as compared to a correspondingantibody generated against the proximal portion of PSMGFR comprising theamino acid sequence of SEQ ID NO. 3 (N-10).
 53. The method of claim 49,wherein said contacting is in vitro.
 54. The method of claim 49, whereinsaid contacting comprises contacting the stem or stem-like cell with asurface comprising said antibody.